MERFISH Report
1. Overview
1.1 Sample Information
A brief sample information is generated from the submission table for the following analysis.
| Batch | Index | Genotype | Data Path | region |
|---|---|---|---|---|
| 1 | 009GFPcre | GFPcre | 202402181603_20240218Julio011n009VZG191m500x01_VMSC00101 | region_1 |
| 1 | 011GFP | GFP | 202402181603_20240218Julio011n009VZG191m500x01_VMSC00101 | region_0 |
| 2 | 724GFP | GFP | 202402181602_20240218Julio724n008VZG191m500x02_VMSC05201 | region_1 |
| 2 | 008GFPcre | GFPcre | 202402181602_20240218Julio724n008VZG191m500x02_VMSC05201 | region_0 |
1.2 MERSCOPE Data Quality Summary
The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.
Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
2. Data Processing & Analysis
2.1 Cell Segmentation
Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.
To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25. After filter the outliers, the qualified cells count is shown in the following table.
Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified 219765 cells across 4 samples.
| Sample Index | Cell Count |
|---|---|
| 724GFP | 64156 |
| 009GFP-cre | 58084 |
| 011GFP | 48946 |
| 008GFP-cre | 48579 |
Identified Cell Spatial Overview on all Samples
2.2 Batch Effect & Dimension Reduction
We use Scanpy for the analysis of single-cell level transcriptome data. The initial stage of our analysis involves the elimination of batch effects, thereby ensuring that different samples from various batches are distributed within the same domain and are statistically reasonable to be integrated and compared. To achieve this, we utilize the Harmony algorithm.
Subsequently, we present visualizations of the batch difference by Leiden UMAP clusters. Also, we illustrate the distributions of the Leiden clusters for future analysis.
Umap of cells and colored by batch
Umap of cells on each batch
Leiden Umap can be dividied to 28 clusters
2.3 Cell Annotation
We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.
The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3). Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.
With the annotation, we can identify and plot the selected types of cells in each sample.
2.3.1 Cell Annotation (Low resolution class)
| class_name | count |
|---|---|
| 31 OPC-Oligo | 44135 |
| 30 Astro-Epen | 32941 |
| 01 IT-ET Glut | 31657 |
| 33 Vascular | 24933 |
| 09 CNU-LGE GABA | 21244 |
| 34 Immune | 13185 |
| 02 NP-CT-L6b Glut | 7995 |
| 27 MY GABA | 4783 |
| 29 CB Glut | 4283 |
| 20 MB GABA | 3398 |
| 18 TH Glut | 3033 |
| 07 CTX-MGE GABA | 2951 |
| 11 CNU-HYa GABA | 2417 |
| 28 CB GABA | 2314 |
| 24 MY Glut | 2150 |
| 32 OEC | 2132 |
| 12 HY GABA | 2048 |
| 19 MB Glut | 1999 |
| 06 CTX-CGE GABA | 1950 |
| 23 P Glut | 1926 |
| 13 CNU-HYa Glut | 1647 |
| 26 P GABA | 1640 |
| 10 LSX GABA | 1258 |
| 08 CNU-MGE GABA | 1253 |
| 05 OB-IMN GABA | 1221 |
| 04 DG-IMN Glut | 440 |
| 14 HY Glut | 230 |
| 17 MH-LH Glut | 154 |
| 03 OB-CR Glut | 152 |
| 22 MB-HB Sero | 109 |
| 21 MB Dopa | 107 |
| 25 Pineal Glut | 52 |
| 16 HY MM Glut | 14 |
| 15 HY Gnrh1 Glut | 14 |
2.3.2 Cell Annotation (High resolution subclass)
| subclass_name | count | |
|---|---|---|
| 18 | 327 Oligo NN | 40218 |
| 4 | 333 Endo NN | 15499 |
| 19 | 319 Astro-TE NN | 13267 |
| 27 | 062 STR D2 Gaba | 12022 |
| 3 | 318 Astro-NT NN | 9823 |
| 84 | 006 L4/5 IT CTX Glut | 8720 |
| 46 | 334 Microglia NN | 7514 |
| 10 | 321 Astroependymal NN | 5968 |
| 284 | 061 STR D1 Gaba | 5384 |
| 40 | 030 L6 CT CTX Glut | 5189 |
| 1 | 314 CB Granule Glut | 3952 |
| 44 | 326 OPC NN | 3917 |
| 7 | 331 Peri NN | 3837 |
| 24 | 004 L6 IT CTX Glut | 3811 |
| 74 | 337 DC NN | 3577 |
| 98 | 007 L2/3 IT CTX Glut | 3208 |
| 6 | 330 VLMC NN | 3104 |
| 107 | 063 STR D1 Sema5a Gaba | 2909 |
| 268 | 151 TH Prkcd Grin2c Glut | 2744 |
| 102 | 005 L5 IT CTX Glut | 2711 |
| 99 | 009 L2/3 IT PIR-ENTl Glut | 2600 |
| 35 | 017 CA3 Glut | 2195 |
| 13 | 328 OEC NN | 2132 |
| 38 | 338 Lymphoid NN | 1820 |
| 12 | 332 SMC NN | 1751 |
| 134 | 022 L5 ET CTX Glut | 1664 |
| 42 | 306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba | 1604 |
| 83 | 052 Pvalb Gaba | 1475 |
| 159 | 053 Sst Gaba | 1244 |
| 8 | 311 CBX MLI Megf11 Gaba | 1201 |
| 148 | 016 CA1-ProS Glut | 1135 |
| 115 | 019 L2/3 IT PPP Glut | 1090 |
| 156 | 012 MEA Slc17a7 Glut | 960 |
| 116 | 029 L6b CTX Glut | 953 |
| 58 | 285 MY Lhx1 Gly-Gaba | 923 |
| 2 | 046 Vip Gaba | 872 |
| 36 | 320 Astro-OLF NN | 860 |
| 174 | 325 CHOR NN | 857 |
| 91 | 181 IC Tfap2d Maf Glut | 855 |
| 94 | 032 L5 NP CTX Glut | 834 |
| 33 | 317 Astro-CB NN | 796 |
| 86 | 198 IC Six3 En2 Gaba | 765 |
| 172 | 093 RT-ZI Gnb3 Gaba | 761 |
| 128 | 228 PSV Pvalb Lhx2 Glut | 761 |
| 11 | 329 ABC NN | 742 |
| 63 | 305 SPVI-SPVC Sall3 Nfib Gly-Gaba | 681 |
| 29 | 101 ZI Pax6 Gaba | 666 |
| 97 | 049 Lamp5 Gaba | 649 |
| 252 | 113 MEA-COA-BMA Ccdc42 Glut | 647 |
| 76 | 073 MEA-BST Sox6 Gaba | 601 |
| 120 | 323 Ependymal NN | 526 |
| 61 | 300 PARN-MDRNd-NTS Gbx2 Gly-Gaba | 517 |
| 145 | 114 COAa-PAA-MEA Barhl2 Glut | 512 |
| 20 | 041 OB-in Frmd7 Gaba | 490 |
| 28 | 203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba | 481 |
| 73 | 069 LSX Nkx2-1 Gaba | 452 |
| 164 | 018 L2 IT PPP-APr Glut | 446 |
| 219 | 168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut | 424 |
| 5 | 316 Bergmann NN | 421 |
| 239 | 037 DG Glut | 415 |
| 14 | 313 CBX Purkinje Gaba | 410 |
| 194 | 014 LA-BLA-BMA-PA Glut | 409 |
| 127 | 246 CU-ECU-SPVI Foxb1 Glut | 403 |
| 54 | 322 Tanycyte NN | 401 |
| 96 | 070 LSX Prdm12 Slit2 Gaba | 399 |
| 65 | 256 SPVC Mafa Glut | 398 |
| 100 | 010 IT AON-TT-DP Glut | 395 |
| 166 | 064 STR-PAL Chst9 Gaba | 375 |
| 195 | 002 IT EP-CLA Glut | 369 |
| 23 | 315 DCO UBC Glut | 331 |
| 143 | 278 NLL Gata3 Gly-Gaba | 322 |
| 17 | 304 NTS-PARN Neurod2 Gly-Gaba | 321 |
| 254 | 001 CLA-EPd-CTX Car3 Glut | 314 |
| 298 | 060 OT D3 Folh1 Gaba | 307 |
| 50 | 235 PG-TRN-LRN Fat2 Glut | 305 |
| 153 | 057 NDB-SI-MA-STRv Lhx8 Gaba | 305 |
| 123 | 279 PSV Pax2 Gly-Gaba | 302 |
| 121 | 080 CEA-AAA-BST Six3 Sp9 Gaba | 294 |
| 225 | 056 Sst Chodl Gaba | 290 |
| 163 | 076 MEA-BST Lhx6 Nfib Gaba | 285 |
| 53 | 222 PB Evx2 Glut | 272 |
| 26 | 308 DCO Il22 Gly-Gaba | 272 |
| 122 | 023 SUB-ProS Glut | 269 |
| 224 | 013 COAp Grxcr2 Glut | 257 |
| 117 | 027 L6b EPd Glut | 256 |
| 15 | 054 STR Prox1 Lhx6 Gaba | 253 |
| 68 | 201 PAG-RN Nkx2-2 Otx1 Gaba | 253 |
| 9 | 312 CBX MLI Cdh22 Gaba | 252 |
| 72 | 033 NP SUB Glut | 250 |
| 52 | 028 L6b/CT ENT Glut | 247 |
| 110 | 255 SPVO Mafa Meis2 Glut | 246 |
| 87 | 197 SNr Six3 Gaba | 242 |
| 25 | 047 Sncg Gaba | 238 |
| 215 | 058 PAL-STR Gaba-Chol | 238 |
| 106 | 254 VCO Mafa Meis2 Glut | 234 |
| 113 | 210 PRT Mecom Gaba | 228 |
| 237 | 026 NLOT Rho Glut | 225 |
| 49 | 045 OB-STR-CTX Inh IMN | 222 |
| 95 | 119 SI-MA-LPO-LHA Skor1 Glut | 222 |
| 105 | 039 OB Meis2 Thsd7b Gaba | 217 |
| 170 | 217 PB Lmx1a Glut | 215 |
| 64 | 245 SPVI-SPVC Tlx3 Ebf3 Glut | 213 |
| 162 | 003 L5/6 IT TPE-ENT Glut | 207 |
| 69 | 243 PGRN-PARN-MDRN Hoxb5 Glut | 207 |
| 226 | 074 MEA-BST Lhx6 Sp9 Gaba | 204 |
| 59 | 025 CA2-FC-IG Glut | 202 |
| 104 | 015 ENTmv-PA-COAp Glut | 196 |
| 31 | 098 AHN-SBPV-PVHd Pdrm12 Gaba | 193 |
| 119 | 048 RHP-COA Ndnf Gaba | 191 |
| 157 | 202 PRT Tcf7l2 Gaba | 187 |
| 34 | 335 BAM NN | 186 |
| 193 | 082 CEA-BST Ebf1 Pdyn Gaba | 177 |
| 71 | 199 PAG-MRN-RN Foxa2 Gaba | 175 |
| 149 | 071 LSX Prdm12 Zeb2 Gaba | 174 |
| 169 | 200 PAG-ND-PCG Onecut1 Gaba | 173 |
| 290 | 055 STR Lhx8 Gaba | 167 |
| 51 | 034 NP PPP Glut | 165 |
| 178 | 265 PB Sst Gly-Gaba | 161 |
| 109 | 153 MG-POL-SGN Nts Glut | 160 |
| 125 | 195 SNr-VTA Pax5 Npas1 Gaba | 145 |
| 150 | 182 CUN-PPN Evx2 Meis2 Glut | 145 |
| 152 | 295 CBN Dmbx1 Gaba | 145 |
| 229 | 090 BST-MPN Six3 Nrgn Gaba | 144 |
| 88 | 277 DTN-LDT-IPN Otp Pax3 Gaba | 142 |
| 210 | 036 HPF CR Glut | 137 |
| 129 | 065 IA Mgp Gaba | 133 |
| 158 | 263 CS-RPO Meis2 Gaba | 127 |
| 16 | 043 OB-mi Frmd7 Gaba | 124 |
| 89 | 270 LDT-DTN Gata3 Nfix Gaba | 121 |
| 93 | 051 Pvalb chandelier Gaba | 121 |
| 37 | 042 OB-out Frmd7 Gaba | 114 |
| 285 | 079 CEA-BST Six3 Cyp26b1 Gaba | 114 |
| 171 | 287 MV-SPIV-PRP Dmbx1 Gly-Gaba | 114 |
| 276 | 059 GPe-SI Sox6 Cyp26b1 Gaba | 114 |
| 62 | 257 SPVC Ccdc172 Glut | 114 |
| 264 | 120 MEA Otp Foxp2 Glut | 113 |
| 160 | 050 Lamp5 Lhx6 Gaba | 111 |
| 155 | 216 MB-MY Tph2 Glut-Sero | 109 |
| 137 | 215 SNc-VTA-RAmb Foxa1 Dopa | 107 |
| 161 | 192 PPN-CUN-PCG Otp En1 Gaba | 105 |
| 133 | 264 PRNc Otp Gly-Gaba | 103 |
| 317 | 183 PBG Mtnr1a Glut-Chol | 103 |
| 48 | 031 CT SUB Glut | 101 |
| 184 | 283 PRP Otp Gly-Gaba | 100 |
| 204 | 068 LSX Otx2 Gaba | 96 |
| 101 | 072 LSX Sall3 Lmo1 Gaba | 96 |
| 41 | 309 CB PLI Gly-Gaba | 95 |
| 244 | 066 NDB-SI-ant Prdm12 Gaba | 93 |
| 286 | 081 ACB-BST-FS D1 Gaba | 90 |
| 243 | 104 TU-ARH Otp Six6 Gaba | 90 |
| 257 | 075 MEA-BST Lhx6 Nr2e1 Gaba | 89 |
| 138 | 336 Monocytes NN | 88 |
| 167 | 196 PAG-PPN Pax5 Sox21 Gaba | 84 |
| 22 | 310 CBX Golgi Gly-Gaba | 84 |
| 67 | 085 SI-MPO-LPO Lhx8 Gaba | 83 |
| 187 | 238 NTS Phox2b Glut | 83 |
| 207 | 233 NLL-SOC Spp1 Glut | 82 |
| 85 | 282 POR Spp1 Gly-Gaba | 79 |
| 77 | 146 LH Pou4f1 Sox1 Glut | 78 |
| 168 | 020 L2/3 IT RSP Glut | 78 |
| 0 | 145 MH Tac2 Glut | 76 |
| 246 | 088 BST Tac2 Gaba | 73 |
| 66 | 258 SPVC Nmu Glut | 72 |
| 142 | 224 PCG-PRNr Vsx2 Nkx6-1 Glut | 69 |
| 130 | 267 CS-PRNr-PCG Tmem163 Otp Gaba | 68 |
| 39 | 208 SC Lef1 Otx2 Gaba | 68 |
| 82 | 213 SCsg Gabrr2 Gaba | 66 |
| 151 | 008 L2/3 IT ENT Glut | 64 |
| 135 | 290 MY Prox1 Lmo7 Gly-Gaba | 64 |
| 205 | 162 CUN Evx2 Lhx2 Glut | 63 |
| 111 | 089 PVR Six3 Sox3 Gaba | 63 |
| 80 | 251 NTS Dbh Glut | 58 |
| 177 | 221 LDT-PCG Vsx2 Lhx4 Glut | 57 |
| 196 | 024 L5 PPP Glut | 56 |
| 248 | 121 MEA-BST Otp Zic2 Glut | 55 |
| 112 | 206 SCm-PAG Cdh23 Gaba | 55 |
| 199 | 194 MRN-VTN-PPN Pax5 Cdh23 Gaba | 54 |
| 176 | 134 PH-ant-LHA Otp Bsx Glut | 54 |
| 30 | 293 PAS-MV Ebf2 Gly-Gaba | 54 |
| 262 | 103 PVHd-DMH Lhx6 Gaba | 53 |
| 55 | 147 AD Serpinb7 Glut | 52 |
| 47 | 262 Pineal Crx Glut | 52 |
| 186 | 109 LGv-ZI Otx2 Gaba | 51 |
| 118 | 011 L2 IT ENT-po Glut | 51 |
| 190 | 271 NI-RPO Gata3 Nr4a2 Gaba | 51 |
| 220 | 209 SCs Pax7 Nfia Gaba | 47 |
| 206 | 205 SC-PAG Lef1 Emx2 Gaba | 45 |
| 57 | 044 OB Dopa-Gaba | 45 |
| 140 | 297 CU-ECU Pax2 Gly-Gaba | 45 |
| 263 | 218 PSV Lmx1a Trpv6 Glut | 44 |
| 108 | 214 IPN Otp Crisp1 Gaba | 42 |
| 154 | 268 CS-PRNr-DR En1 Sox2 Gaba | 42 |
| 136 | 169 PAG-SC Pou4f1 Zic1 Glut | 41 |
| 45 | 067 LSX Sall3 Pax6 Gaba | 41 |
| 218 | 207 SCs Dmbx1 Gaba | 40 |
| 234 | 100 AHN Onecut3 Gaba | 40 |
| 245 | 299 MARN-PPY Ngfr Gly-Gaba | 39 |
| 81 | 276 LDT-PCG St18 Gaba | 38 |
| 90 | 204 SC Otx2 Gcnt4 Gaba | 34 |
| 114 | 172 PAG Pou4f1 Ebf2 Glut | 33 |
| 201 | 154 PF Fzd5 Glut | 33 |
| 180 | 212 SCs Lef1 Gli3 Gaba | 32 |
| 266 | 107 DMH Hmx2 Gaba | 32 |
| 208 | 086 MPO-ADP Lhx8 Gaba | 32 |
| 202 | 083 CEA-BST Rai14 Pdyn Crh Gaba | 32 |
| 203 | 141 PH-SUM Foxa1 Glut | 32 |
| 175 | 193 MRN-PPN-CUN Pax8 Gaba | 31 |
| 211 | 170 PAG-MRN Tfap2b Glut | 30 |
| 213 | 288 MDRN Hoxb5 Ebf2 Gly-Gaba | 29 |
| 200 | 174 PAG Pou4f2 Mesi2 Glut | 29 |
| 131 | 211 SC Tnnt1 Gli3 Gaba | 29 |
| 278 | 108 ARH-PVp Tbx3 Gaba | 28 |
| 249 | 115 MS-SF Bsx Glut | 27 |
| 43 | 275 PDTg Otp Olig3 Gaba | 27 |
| 181 | 102 DMH-LHA Gsx1 Gaba | 27 |
| 212 | 180 SCiw Pitx2 Glut | 26 |
| 240 | 234 MEV Ppp1r1c Glut | 26 |
| 189 | 250 CBN Neurod2 Pvalb Glut | 26 |
| 141 | 286 PPY-PGRNl Vip Glyc-Gaba | 26 |
| 288 | 106 PVpo-VMPO-MPN Hmx2 Gaba | 25 |
| 21 | 021 L4 RSP-ACA Glut | 25 |
| 78 | 038 DG-PIR Ex IMN | 25 |
| 126 | 261 HB Calcb Chol | 25 |
| 60 | 229 PB-NTS Phox2b Ebf3 Lmx1b Glut | 24 |
| 214 | 248 MV-SPIV Zic4 Neurod2 Glut | 24 |
| 183 | 133 PVH-SO-PVa Otp Glut | 24 |
| 92 | 303 IRN Dmbx1 Pax2 Gly-Gaba | 24 |
| 227 | 177 SCig-an-PPT Foxb1 Glut | 24 |
| 231 | 160 PAG-SC Neurod2 Meis2 Glut | 24 |
| 232 | 226 PRNc-PARN Tlx1 Glut | 24 |
| 173 | 124 MPN-MPO-PVpo Hmx2 Glut | 24 |
| 287 | 135 STN-PSTN Pitx2 Glut | 24 |
| 147 | 324 Hypendymal NN | 22 |
| 241 | 129 VMH Nr5a1 Glut | 21 |
| 269 | 149 PVT-PT Ntrk1 Glut | 21 |
| 260 | 273 PDTg-PCG Pax6 Gaba | 21 |
| 228 | 173 PAG Pou4f2 Glut | 21 |
| 293 | 112 GPi Tbr1 Cngb3 Gaba-Glut | 21 |
| 146 | 187 SCsg Pde5a Glut | 20 |
| 256 | 105 TMd-DMH Foxd2 Gaba | 19 |
| 292 | 272 LDT-PCG-CS Gata3 Lhx1 Gaba | 18 |
| 70 | 132 AHN-RCH-LHA Otp Fezf1 Glut | 17 |
| 308 | 122 LHA-MEA Otp Glut | 17 |
| 32 | 302 MV Xdh Gly-Gaba | 17 |
| 75 | 191 PAG-MRN Rln3 Gaba | 17 |
| 182 | 167 PRC-PAG Tcf7l2 Irx2 Glut | 17 |
| 259 | 094 SCH Six6 Cdc14a Gaba | 16 |
| 103 | 225 PRNc-NI-SG-RPO Vsx2 Nr4a2 Glut | 16 |
| 216 | 188 SCop Sln Glut | 16 |
| 139 | 231 IPN-LDT Vsx2 Nkx6-1 Glut | 16 |
| 165 | 291 NTS-MDRNd Prox1 Zic1 Gly-Gaba | 16 |
| 291 | 099 SBPV-PVa Six6 Satb2 Gaba | 15 |
| 282 | 087 MPN-MPO-LPO Lhx6 Zfhx3 Gaba | 15 |
| 255 | 035 OB Eomes Ms4a15 Glut | 15 |
| 271 | 097 PVHd-SBPV Six3 Prox1 Gaba | 15 |
| 280 | 284 GRN-IRN-MDRNd Ikzf1 Gly-Gaba | 14 |
| 265 | 296 RPA Pax6 Hoxb5 Gly-Gaba | 14 |
| 275 | 152 RE-Xi Nox4 Glut | 14 |
| 209 | 142 HY Gnrh1 Glut | 14 |
| 198 | 247 MV-SPIV Phox2b Ebf3 Lbx1 Glut | 14 |
| 222 | 298 PRP Gata3 Slc6a5 Gly-Gaba | 13 |
| 79 | 111 TRS-BAC Sln Glut | 13 |
| 267 | 155 PRC-PAG Pax6 Glut | 13 |
| 192 | 176 SCig Foxb1 Glut | 13 |
| 185 | 144 MM Foxb1 Glut | 12 |
| 132 | 178 SCig Foxb1 Otx2 Glut | 12 |
| 188 | 281 POR Gata3 Gly-Gaba | 11 |
| 221 | 171 PAG Pou4f1 Bnc2 Glut | 11 |
| 217 | 237 PRP-NI-PRNc-GRN Otp Glut | 11 |
| 302 | 078 SI-MA-ACB Ebf1 Bnc2 Gaba | 11 |
| 301 | 232 LDT Vsx2 Nkx6-1 Nfib Glut | 10 |
| 296 | 084 BST-SI-AAA Six3 Slc22a3 Gaba | 10 |
| 247 | 227 PB-PSV Phox2b Glut | 10 |
| 235 | 220 PB Pax5 Glut | 9 |
| 258 | 117 LHA Barhl2 Glut | 9 |
| 197 | 223 B-PB Nr4a2 Glut | 9 |
| 299 | 040 OB Trdn Gaba | 9 |
| 289 | 307 RO-RPA Pkd2l1 Gaba | 9 |
| 233 | 165 PAG-MRN Pou3f1 Glut | 9 |
| 273 | 244 MV-SPIV Slc6a2 Glut | 8 |
| 179 | 175 SC Bnc2 Glut | 8 |
| 144 | 140 PMd-LHA Foxb1 Glut | 8 |
| 303 | 077 CEA-BST Gal Avp Gaba | 7 |
| 272 | 252 DMX VII Tbx20 Chol | 7 |
| 253 | 159 IF-RL-CLI-PAG Foxa1 Glut | 7 |
| 251 | 301 MV Nr4a2 Gly-Gaba | 6 |
| 283 | 091 ARH-PVi Six6 Dopa-Gaba | 6 |
| 238 | 123 DMH Nkx2-4 Glut | 6 |
| 316 | 294 MV Pax6 Gly-Gaba | 6 |
| 300 | 161 PAG Pou4f3 Glut | 6 |
| 261 | 128 VMH Fezf1 Glut | 6 |
| 294 | 092 TMv-PMv Tbx3 Hist-Gaba | 6 |
| 191 | 136 PMv-TMv Pitx2 Glut | 5 |
| 223 | 156 MB-ant-ve Dmrta2 Glut | 5 |
| 274 | 148 AV Col27a1 Glut | 5 |
| 277 | 150 CM-IAD-CL-PCN Sema5b Glut | 4 |
| 315 | 118 ADP-MPO Trp73 Glut | 4 |
| 279 | 269 LDT Fgf7 Gaba | 4 |
| 56 | 190 ND-INC Foxd2 Glut | 4 |
| 321 | 116 AVPV-MEPO-SFO Tbr1 Glut | 4 |
| 295 | 236 IRN Vip Glut | 3 |
| 297 | 096 PVHd Gsc Gaba | 3 |
| 270 | 164 APN C1ql4 Glut | 3 |
| 314 | 157 RN Spp1 Glut | 3 |
| 313 | 166 MRN Pou3f1 C1ql4 Glut | 3 |
| 306 | 110 BST-po Iigp1 Glut | 3 |
| 307 | 139 PH-LHA Foxb1 Glut | 3 |
| 311 | 230 PRNr Otp Nfib Glut | 2 |
| 318 | 280 NLL-po Pax7 Gaba | 2 |
| 312 | 143 MM-ant Foxb1 Glut | 2 |
| 242 | 126 ARH-PVp Tbx3 Glut | 2 |
| 310 | 138 PH Pitx2 Glut | 2 |
| 305 | 095 DMH Prdm13 Gaba | 2 |
| 124 | 185 SCig Tfap2b Chrnb3 Glut | 2 |
| 230 | 186 SCop Pou4f2 Neurod2 Glut | 2 |
| 250 | 260 MDRNv Crp Glut | 2 |
| 309 | 189 PAG Ucn Glut | 1 |
| 304 | 239 MARN-GRN Pyy Glut | 1 |
| 281 | 292 MV Nkx6-1 Gly-Gaba | 1 |
| 319 | 249 NTS Aldh1a2 Glut | 1 |
| 320 | 289 MDRNd Prox1 Pax6 Gly-Gaba | 1 |
| 236 | 130 LHA Pmch Glut | 1 |
| 322 | 274 PDTg Otp Shroom3 Gaba | 1 |
| 323 | 137 PH-an Pitx2 Glut | 1 |
| 324 | 219 PB-SUT Tlx3 Lhx2 Glut | 1 |
2.3.3 Spatial cell type (Neurons)
2.3.4 Spatial cell type (Non-Neurons)
3. Gene differentiation
3.1 koGFP v.s. GFPcre
Here, we use Wilcoxon rank-sum to compute differential expression.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.
Cell amount compare: ‘GFP-cre’: 113102, ‘GFP’: 106663.
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 18 | App | 44.736282 | 5.972642 | 0 | 0 |
| 10 | Plp1 | 49.036137 | 5.718488 | 0 | 0 |
| 499 | Cd74 | -59.552753 | -4.692116 | 0 | 0 |
| 9 | Syp | 50.261590 | 3.794836 | 0 | 0 |
| 5 | Cx3cl1 | 51.666542 | 2.978154 | 0 | 0 |
| 14 | Nr4a1 | 45.554310 | 2.809042 | 0 | 0 |
| 35 | Dnm1 | 36.316257 | 2.760810 | 0 | 0 |
| 492 | C3 | -17.730808 | -2.572384 | 0 | 0 |
| 495 | Serpina3n | -24.721464 | -2.536104 | 0 | 0 |
| 76 | Cldn11 | 26.102417 | 2.483486 | 0 | 0 |
| 12 | Arc | 47.141872 | 2.393958 | 0 | 0 |
| 22 | Egr1 | 42.227780 | 2.354570 | 0 | 0 |
| 496 | C4b | -37.432564 | -2.293783 | 0 | 0 |
| 481 | Itgal | -10.370717 | -2.274252 | 0 | 0 |
| 497 | Ctss | -44.824154 | -2.194577 | 0 | 0 |
| 13 | Hpca | 45.568264 | 2.185736 | 0 | 0 |
| 7 | Camk2a | 51.449840 | 2.146260 | 0 | 0 |
| 475 | Cxcl10 | -8.422120 | -2.045975 | 0 | 0 |
| 19 | Eno2 | 44.523117 | 2.018411 | 0 | 0 |
| 15 | Bcan | 45.452614 | 1.913053 | 0 | 0 |
| 2 | Rph3a | 57.176254 | 1.886615 | 0 | 0 |
| 491 | Ly9 | -17.487762 | -1.883386 | 0 | 0 |
| 23 | Gria2 | 42.109333 | 1.831859 | 0 | 0 |
| 486 | Clec7a | -12.054828 | -1.825047 | 0 | 0 |
| 39 | Bsg | 34.559450 | 1.807745 | 0 | 0 |
| 29 | Syngap1 | 38.492718 | 1.746275 | 0 | 0 |
| 0 | Cspg5 | 72.560670 | 1.717004 | 0 | 0 |
| 17 | Grin2b | 45.100048 | 1.701919 | 0 | 0 |
| 4 | Fam131a | 53.949270 | 1.689317 | 0 | 0 |
| 97 | Apoe | 19.690727 | -1.685822 | 0 | 0 |
| 31 | Gria1 | 37.508610 | 1.675839 | 0 | 0 |
| 68 | Egr4 | 26.828337 | 1.653498 | 0 | 0 |
| 8 | Bin1 | 50.626930 | 1.589708 | 0 | 0 |
| 487 | Cst7 | -12.510269 | -1.582236 | 0 | 0 |
| 480 | Lgals3 | -9.810495 | -1.578655 | 0 | 0 |
| 27 | Cplx1 | 39.918278 | 1.556089 | 0 | 0 |
| 114 | Egr2 | 16.973430 | 1.551940 | 0 | 0 |
| 60 | Fos | 29.335768 | 1.530916 | 0 | 0 |
| 498 | Gfap | -59.169655 | -1.496276 | 0 | 0 |
| 24 | Dlg4 | 41.551414 | 1.495855 | 0 | 0 |
| 74 | Olig1 | 26.309402 | 1.414519 | 0 | 0 |
| 25 | Enpp2 | 40.683018 | 1.389329 | 0 | 0 |
| 72 | Grin1 | 26.615938 | 1.379400 | 0 | 0 |
| 26 | Adrb1 | 40.252403 | 1.307181 | 0 | 0 |
| 150 | Fosb | 13.704445 | 1.267708 | 0 | 0 |
| 30 | Grin2a | 38.490376 | 1.260622 | 0 | 0 |
| 102 | Slc17a7 | 18.938023 | 1.256663 | 0 | 0 |
| 494 | C1qa | -22.363613 | -1.247561 | 0 | 0 |
| 36 | Nefm | 35.932125 | 1.214934 | 0 | 0 |
| 3 | Sox8 | 56.846880 | 1.198911 | 0 | 0 |
| 81 | Fosl2 | 24.503006 | 1.174972 | 0 | 0 |
| 6 | Pcdh9 | 51.520077 | 1.172719 | 0 | 0 |
| 58 | Mog | 29.780993 | 1.172717 | 0 | 0 |
| 16 | Mapt | 45.247490 | 1.171918 | 0 | 0 |
| 47 | Kcnc1 | 32.310510 | 1.171672 | 0 | 0 |
| 38 | Grm4 | 34.620040 | 1.070396 | 0 | 0 |
| 163 | Otof | 12.611641 | 1.066515 | 0 | 0 |
| 41 | Syn1 | 34.270800 | 1.046408 | 0 | 0 |
| 108 | Nr4a2 | 18.551891 | 1.038631 | 0 | 0 |
| 48 | Nptxr | 32.190388 | 1.007296 | 0 | 0 |
3.2 Microglia (GFP-cre v.s. GFP)
Here, we use Wilcoxon rank-sum to compute differential expression in Microglia cells.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.
Cell number: ‘GFP’: 4408, ‘GFP-cre’: 3106.
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 490 | Apoe | -13.160284 | -22.351469 | 0.0000000 | 0.0000000 |
| 499 | Cd74 | -38.976810 | -13.935299 | 0.0000000 | 0.0000000 |
| 0 | Cx3cr1 | 26.206287 | 7.033817 | 0.0000000 | 0.0000000 |
| 498 | C4b | -26.623106 | -6.578667 | 0.0000000 | 0.0000000 |
| 2 | Selplg | 20.464607 | 6.321182 | 0.0000000 | 0.0000000 |
| 497 | Ctss | -19.661251 | -6.129716 | 0.0000000 | 0.0000000 |
| 494 | C3 | -15.745511 | -5.026065 | 0.0000000 | 0.0000000 |
| 492 | Cst7 | -14.186185 | -4.969236 | 0.0000000 | 0.0000000 |
| 1 | Tmem119 | 23.285162 | 4.661632 | 0.0000000 | 0.0000000 |
| 482 | Lgals3 | -8.555458 | -4.631769 | 0.0000000 | 0.0000000 |
| 8 | Csf1r | 11.874363 | 4.079345 | 0.0000000 | 0.0000000 |
| 460 | Cxcl10 | -3.207307 | -3.755650 | 0.0013398 | 0.0066992 |
| 486 | Spp1 | -9.400478 | -3.616108 | 0.0000000 | 0.0000000 |
| 480 | Itgal | -8.187654 | -3.544304 | 0.0000000 | 0.0000000 |
| 493 | Itgax | -14.559648 | -3.468330 | 0.0000000 | 0.0000000 |
| 463 | Serpina3n | -3.701132 | -3.420096 | 0.0002146 | 0.0011665 |
| 479 | Clec7a | -7.250827 | -3.344504 | 0.0000000 | 0.0000000 |
| 495 | Csf1 | -16.713840 | -3.097090 | 0.0000000 | 0.0000000 |
| 481 | Cxcl2 | -8.319359 | -3.043944 | 0.0000000 | 0.0000000 |
| 484 | Xdh | -9.306241 | -2.891892 | 0.0000000 | 0.0000000 |
| 489 | Ctsb | -12.294172 | -2.877592 | 0.0000000 | 0.0000000 |
| 488 | Gpc3 | -9.518273 | -2.734765 | 0.0000000 | 0.0000000 |
| 453 | Cd8a | -2.680199 | -2.181966 | 0.0073578 | 0.0309153 |
| 465 | Fmo1 | -3.818512 | -2.171021 | 0.0001343 | 0.0007543 |
| 496 | Gfap | -17.119291 | -2.134081 | 0.0000000 | 0.0000000 |
| 491 | Ly9 | -13.968450 | -1.968051 | 0.0000000 | 0.0000000 |
| 485 | Rgs12 | -9.392124 | -1.915597 | 0.0000000 | 0.0000000 |
| 487 | Ddit3 | -9.515569 | -1.732437 | 0.0000000 | 0.0000000 |
| 461 | Neu4 | -3.387595 | -1.702926 | 0.0007051 | 0.0036723 |
| 462 | Tnf | -3.400176 | -1.643806 | 0.0006734 | 0.0035443 |
| 483 | Cd83 | -8.730924 | -1.618328 | 0.0000000 | 0.0000000 |
| 4 | Camk2a | 13.917956 | 1.606004 | 0.0000000 | 0.0000000 |
| 6 | Syp | 13.472908 | 1.558124 | 0.0000000 | 0.0000000 |
| 11 | Hpca | 10.603275 | 1.402991 | 0.0000000 | 0.0000000 |
| 9 | Rph3a | 11.841915 | 1.400866 | 0.0000000 | 0.0000000 |
| 26 | Cspg5 | 7.203558 | 1.310284 | 0.0000000 | 0.0000000 |
| 466 | Kit | -4.009469 | -1.295562 | 0.0000609 | 0.0003580 |
| 458 | Rspo1 | -3.157602 | -1.279444 | 0.0015907 | 0.0077977 |
| 18 | Bcan | 8.361877 | 1.263355 | 0.0000000 | 0.0000000 |
| 470 | Atf3 | -4.577908 | -1.232095 | 0.0000047 | 0.0000305 |
| 3 | Siglech | 14.975441 | 1.175270 | 0.0000000 | 0.0000000 |
| 48 | Nr4a1 | 4.486057 | 1.162832 | 0.0000073 | 0.0000459 |
| 5 | P2ry12 | 13.843489 | 1.154090 | 0.0000000 | 0.0000000 |
| 13 | Dnm1 | 9.099365 | 1.148387 | 0.0000000 | 0.0000000 |
| 455 | Egr2 | -2.822682 | -1.144313 | 0.0047624 | 0.0212606 |
| 41 | App | 4.928330 | 1.136704 | 0.0000008 | 0.0000060 |
| 477 | Itpr2 | -6.039866 | -1.116609 | 0.0000000 | 0.0000000 |
| 20 | Fam131a | 8.053680 | 1.078608 | 0.0000000 | 0.0000000 |
| 473 | Bcl11b | -4.971124 | -1.075480 | 0.0000007 | 0.0000050 |
| 12 | Eno2 | 10.375032 | 1.073601 | 0.0000000 | 0.0000000 |
| 37 | Cx3cl1 | 5.368049 | 1.068547 | 0.0000001 | 0.0000006 |
| 478 | Bcl6 | -6.933073 | -1.058754 | 0.0000000 | 0.0000000 |
| 69 | Neto1 | 2.708440 | 1.054087 | 0.0067600 | 0.0291381 |
| 7 | Dlg4 | 12.360530 | 1.042307 | 0.0000000 | 0.0000000 |
| 29 | Arc | 6.311123 | 1.030949 | 0.0000000 | 0.0000000 |
3.3 Endothelia cells (GFP-cre v.s. GFP)
Here, we use Wilcoxon rank-sum to compute differential expression in Endothelia cells.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.
Cell number: ‘GFP-cre’: 8497, ‘GFP’: 7002.
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 4 | Bsg | 17.046259 | 7.096224 | 0.0000000 | 0.0000000 |
| 1 | Cldn5 | 19.304459 | 4.063761 | 0.0000000 | 0.0000000 |
| 498 | Cd74 | -8.365247 | -2.673357 | 0.0000000 | 0.0000000 |
| 0 | Flt1 | 23.034956 | 2.247791 | 0.0000000 | 0.0000000 |
| 21 | Nr4a1 | 7.165558 | 2.043065 | 0.0000000 | 0.0000000 |
| 5 | Apoe | 15.964951 | 1.785722 | 0.0000000 | 0.0000000 |
| 9 | App | 11.192018 | 1.747558 | 0.0000000 | 0.0000000 |
| 499 | Gfap | -14.007896 | -1.482300 | 0.0000000 | 0.0000000 |
| 59 | Fos | 4.055646 | 1.470903 | 0.0000500 | 0.0003846 |
| 493 | C4b | -3.615977 | -1.387801 | 0.0002992 | 0.0021072 |
| 28 | Egr1 | 6.308252 | 1.109528 | 0.0000000 | 0.0000000 |
| 494 | Ctss | -3.975957 | -1.091061 | 0.0000701 | 0.0005231 |
| 12 | Synpo2 | 10.440583 | 1.074914 | 0.0000000 | 0.0000000 |
| 2 | Ctnnb1 | 18.271220 | 1.005527 | 0.0000000 | 0.0000000 |
3.4 CA1 (GFP-cre v.s. GFP)
Here, we use Wilcoxon rank-sum to compute differential expression in CA1 cells.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.
Cell number: ‘GFP-cre’: 862, ‘GFP’: 273.
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 0 | Hpca | 13.111697 | 20.114042 | 0.0000000 | 0.0000000 |
| 22 | Gria1 | 7.589025 | 15.772917 | 0.0000000 | 0.0000000 |
| 495 | Nptxr | -10.765465 | -15.584857 | 0.0000000 | 0.0000000 |
| 1 | Fam131a | 11.959662 | 11.401796 | 0.0000000 | 0.0000000 |
| 4 | Grin2a | 11.653724 | 11.238268 | 0.0000000 | 0.0000000 |
| 2 | Ptk2b | 11.802985 | 11.177084 | 0.0000000 | 0.0000000 |
| 10 | Camk2a | 10.252531 | 11.152108 | 0.0000000 | 0.0000000 |
| 499 | Col6a1 | -12.229265 | -11.023427 | 0.0000000 | 0.0000000 |
| 12 | Dkk3 | 10.181343 | 9.752980 | 0.0000000 | 0.0000000 |
| 5 | Arc | 11.546942 | 9.558531 | 0.0000000 | 0.0000000 |
| 15 | Nr4a1 | 8.905788 | 9.050091 | 0.0000000 | 0.0000000 |
| 7 | Wfs1 | 11.329247 | 7.839121 | 0.0000000 | 0.0000000 |
| 65 | App | 3.202817 | 7.816557 | 0.0013609 | 0.0075606 |
| 11 | Egr1 | 10.182191 | 7.584926 | 0.0000000 | 0.0000000 |
| 14 | Cx3cl1 | 9.515970 | 7.312509 | 0.0000000 | 0.0000000 |
| 23 | Grin2b | 7.548241 | 7.112894 | 0.0000000 | 0.0000000 |
| 32 | Gria2 | 5.897891 | 6.622412 | 0.0000000 | 0.0000000 |
| 29 | Cpne6 | 6.761891 | 6.337827 | 0.0000000 | 0.0000000 |
| 39 | Grin1 | 5.297138 | 6.221646 | 0.0000001 | 0.0000011 |
| 3 | Kcnab1 | 11.668873 | 6.177465 | 0.0000000 | 0.0000000 |
| 40 | Syp | 5.153067 | 6.095230 | 0.0000003 | 0.0000024 |
| 6 | Bcan | 11.405944 | 5.269656 | 0.0000000 | 0.0000000 |
| 8 | Gm2115 | 11.292594 | 5.015296 | 0.0000000 | 0.0000000 |
| 47 | Syngap1 | 4.830179 | 4.747772 | 0.0000014 | 0.0000110 |
| 497 | Nr2f2 | -11.678724 | -4.695108 | 0.0000000 | 0.0000000 |
| 498 | Nnat | -12.216023 | -4.622992 | 0.0000000 | 0.0000000 |
| 69 | Dnm1 | 2.954613 | 4.499082 | 0.0031306 | 0.0161372 |
| 493 | Crtac1 | -9.447854 | -4.447514 | 0.0000000 | 0.0000000 |
| 491 | Grp | -8.558642 | -4.210013 | 0.0000000 | 0.0000000 |
| 45 | Eno2 | 4.954228 | 4.128691 | 0.0000007 | 0.0000061 |
| 494 | Adgra1 | -10.327109 | -3.981628 | 0.0000000 | 0.0000000 |
| 479 | Cd74 | -3.730581 | -3.966161 | 0.0001910 | 0.0011508 |
| 478 | Nptx1 | -3.711302 | -3.910166 | 0.0002062 | 0.0012274 |
| 496 | Plagl1 | -11.552451 | -3.754816 | 0.0000000 | 0.0000000 |
| 20 | Itga7 | 7.788182 | 3.707352 | 0.0000000 | 0.0000000 |
| 21 | Egr4 | 7.634048 | 3.522362 | 0.0000000 | 0.0000000 |
| 9 | Epha7 | 11.154562 | 3.462725 | 0.0000000 | 0.0000000 |
| 489 | Hrh3 | -7.111580 | -3.399637 | 0.0000000 | 0.0000000 |
| 481 | Oxtr | -3.924017 | -3.322877 | 0.0000871 | 0.0005443 |
| 24 | Rbfox3 | 7.177471 | 3.254410 | 0.0000000 | 0.0000000 |
| 488 | Trib2 | -5.944926 | -3.246603 | 0.0000000 | 0.0000000 |
| 28 | Epha10 | 6.863376 | 3.198907 | 0.0000000 | 0.0000000 |
| 36 | Lct | 5.597991 | 3.186000 | 0.0000000 | 0.0000002 |
| 492 | Gfap | -9.152086 | -3.083316 | 0.0000000 | 0.0000000 |
| 17 | Kcnd2 | 8.110752 | 2.968716 | 0.0000000 | 0.0000000 |
| 16 | Neurod6 | 8.615953 | 2.950619 | 0.0000000 | 0.0000000 |
| 25 | Kcnh7 | 7.124398 | 2.666600 | 0.0000000 | 0.0000000 |
| 60 | Dlg4 | 4.006752 | 2.657844 | 0.0000616 | 0.0003946 |
| 490 | Nos1 | -7.155966 | -2.643271 | 0.0000000 | 0.0000000 |
| 480 | Ly6g6e | -3.764269 | -2.631040 | 0.0001670 | 0.0010311 |
| 18 | Nr4a2 | 7.983525 | 2.622531 | 0.0000000 | 0.0000000 |
| 462 | Ctss | -2.671133 | -2.616871 | 0.0075596 | 0.0343617 |
| 464 | Otof | -2.732151 | -2.566950 | 0.0062922 | 0.0291307 |
| 54 | Lratd2 | 4.322436 | 2.529932 | 0.0000154 | 0.0001087 |
| 35 | Gpr63 | 5.660386 | 2.527436 | 0.0000000 | 0.0000002 |
| 44 | Brinp1 | 5.045332 | 2.523550 | 0.0000005 | 0.0000038 |
| 13 | Nefm | 10.026256 | 2.517317 | 0.0000000 | 0.0000000 |
| 52 | Zbtb20 | 4.493308 | 2.417756 | 0.0000070 | 0.0000508 |
| 27 | Cck | 6.973759 | 2.368450 | 0.0000000 | 0.0000000 |
| 58 | Col11a1 | 4.087050 | 2.331447 | 0.0000437 | 0.0002874 |
| 460 | Mfsd2a | -2.636598 | -2.330735 | 0.0083742 | 0.0373848 |
| 33 | Drd5 | 5.788672 | 2.164355 | 0.0000000 | 0.0000001 |
| 26 | Gabra1 | 6.996853 | 2.135416 | 0.0000000 | 0.0000000 |
| 472 | Myh11 | -2.939464 | -1.960730 | 0.0032878 | 0.0167745 |
| 34 | Scn4b | 5.688247 | 1.931303 | 0.0000000 | 0.0000001 |
| 470 | Npy | -2.914146 | -1.931014 | 0.0035666 | 0.0178332 |
| 19 | Bcl6 | 7.972931 | 1.893637 | 0.0000000 | 0.0000000 |
| 62 | Wnt2 | 3.601977 | 1.877229 | 0.0003158 | 0.0018577 |
| 59 | Fos | 4.041393 | 1.874660 | 0.0000531 | 0.0003450 |
| 48 | Sorl1 | 4.787488 | 1.810903 | 0.0000017 | 0.0000134 |
| 56 | Meis2 | 4.131754 | 1.765681 | 0.0000360 | 0.0002432 |
| 63 | Gria3 | 3.438203 | 1.668010 | 0.0005856 | 0.0033655 |
| 476 | Grin3a | -3.237775 | -1.643861 | 0.0012047 | 0.0067677 |
| 38 | Lmo1 | 5.439196 | 1.643091 | 0.0000001 | 0.0000005 |
| 31 | Pkp2 | 6.021940 | 1.642286 | 0.0000000 | 0.0000000 |
| 477 | Deptor | -3.480153 | -1.526833 | 0.0005011 | 0.0029135 |
| 61 | Adgrl2 | 3.754840 | 1.520386 | 0.0001735 | 0.0010576 |
| 41 | Crhr1 | 5.131668 | 1.517439 | 0.0000003 | 0.0000026 |
| 55 | Plekhg1 | 4.233664 | 1.514918 | 0.0000230 | 0.0001597 |
| 70 | Hs3st1 | 2.847513 | 1.484375 | 0.0044062 | 0.0213894 |
| 46 | Htr1a | 4.897871 | 1.425808 | 0.0000010 | 0.0000079 |
| 30 | Bcl11b | 6.415380 | 1.420154 | 0.0000000 | 0.0000000 |
| 484 | Fam107a | -4.499664 | -1.401763 | 0.0000068 | 0.0000507 |
| 72 | Bin1 | 2.598250 | 1.345265 | 0.0093700 | 0.0414603 |
| 37 | Ctsb | 5.486760 | 1.334361 | 0.0000000 | 0.0000004 |
| 50 | Adrb1 | 4.590556 | 1.333000 | 0.0000044 | 0.0000340 |
| 485 | Tpbg | -4.566297 | -1.305343 | 0.0000050 | 0.0000376 |
| 461 | Lrrc55 | -2.646450 | -1.292745 | 0.0081342 | 0.0366403 |
| 465 | Bsg | -2.739037 | -1.287415 | 0.0061620 | 0.0287942 |
| 67 | Car4 | 3.034381 | 1.261995 | 0.0024103 | 0.0126858 |
| 487 | Tcerg1l | -5.172665 | -1.253383 | 0.0000002 | 0.0000022 |
| 483 | Cnr1 | -4.227625 | -1.239971 | 0.0000236 | 0.0001618 |
| 469 | Tacr3 | -2.900692 | -1.232076 | 0.0037234 | 0.0184326 |
| 71 | Ndst4 | 2.795288 | 1.222578 | 0.0051854 | 0.0246922 |
| 49 | Smad3 | 4.750517 | 1.199729 | 0.0000020 | 0.0000159 |
| 53 | Robo1 | 4.462269 | 1.194761 | 0.0000081 | 0.0000579 |
| 57 | Npy2r | 4.110038 | 1.188083 | 0.0000396 | 0.0002637 |
| 43 | Fibcd1 | 5.052112 | -1.187138 | 0.0000004 | 0.0000038 |
| 466 | Ccl6 | -2.757681 | -1.085428 | 0.0058213 | 0.0274589 |
| 473 | Igfbp6 | -3.081628 | -1.022652 | 0.0020587 | 0.0109506 |
4. Hippocampal Region
4.1 Hippocampal Region Selection
| Counts | |
|---|---|
| 724GFP | 5430 |
| 011GFP | 3695 |
| 009GFP-cre | 2495 |
| 008GFP-cre | 4294 |
4.2 Cell Types in Hippo
| subclass_name | count | |
|---|---|---|
| 2 | 327 Oligo NN | 2011 |
| 92 | 337 DC NN | 1445 |
| 127 | 062 STR D2 Gaba | 1272 |
| 3 | 319 Astro-TE NN | 1159 |
| 14 | 334 Microglia NN | 1104 |
| 4 | 333 Endo NN | 963 |
| 79 | 017 CA3 Glut | 747 |
| 64 | 016 CA1-ProS Glut | 745 |
| 6 | 321 Astroependymal NN | 492 |
| 90 | 009 L2/3 IT PIR-ENTl Glut | 440 |
| 61 | 338 Lymphoid NN | 431 |
| 0 | 318 Astro-NT NN | 408 |
| 8 | 326 OPC NN | 336 |
| 1 | 331 Peri NN | 271 |
| 155 | 061 STR D1 Gaba | 257 |
| 63 | 037 DG Glut | 245 |
| 154 | 063 STR D1 Sema5a Gaba | 185 |
| 46 | 330 VLMC NN | 180 |
| 5 | 328 OEC NN | 134 |
| 74 | 025 CA2-FC-IG Glut | 129 |
| 42 | 010 IT AON-TT-DP Glut | 120 |
| 29 | 332 SMC NN | 96 |
| 249 | 026 NLOT Rho Glut | 87 |
| 215 | 114 COAa-PAA-MEA Barhl2 Glut | 79 |
| 174 | 057 NDB-SI-MA-STRv Lhx8 Gaba | 72 |
| 238 | 120 MEA Otp Foxp2 Glut | 70 |
| 73 | 023 SUB-ProS Glut | 67 |
| 150 | 073 MEA-BST Sox6 Gaba | 63 |
| 7 | 285 MY Lhx1 Gly-Gaba | 61 |
| 57 | 119 SI-MA-LPO-LHA Skor1 Glut | 56 |
| 140 | 007 L2/3 IT CTX Glut | 53 |
| 70 | 030 L6 CT CTX Glut | 52 |
| 20 | 306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba | 50 |
| 34 | 006 L4/5 IT CTX Glut | 49 |
| 100 | 012 MEA Slc17a7 Glut | 49 |
| 144 | 335 BAM NN | 48 |
| 82 | 320 Astro-OLF NN | 47 |
| 172 | 060 OT D3 Folh1 Gaba | 45 |
| 112 | 013 COAp Grxcr2 Glut | 43 |
| 71 | 028 L6b/CT ENT Glut | 42 |
| 69 | 069 LSX Nkx2-1 Gaba | 36 |
| 72 | 046 Vip Gaba | 36 |
| 27 | 329 ABC NN | 34 |
| 85 | 064 STR-PAL Chst9 Gaba | 34 |
| 68 | 049 Lamp5 Gaba | 34 |
| 32 | 052 Pvalb Gaba | 34 |
| 94 | 304 NTS-PARN Neurod2 Gly-Gaba | 33 |
| 134 | 048 RHP-COA Ndnf Gaba | 32 |
| 80 | 058 PAL-STR Gaba-Chol | 32 |
| 108 | 019 L2/3 IT PPP Glut | 32 |
| 116 | 004 L6 IT CTX Glut | 32 |
| 170 | 056 Sst Chodl Gaba | 31 |
| 171 | 080 CEA-AAA-BST Six3 Sp9 Gaba | 30 |
| 106 | 070 LSX Prdm12 Slit2 Gaba | 29 |
| 62 | 033 NP SUB Glut | 26 |
| 101 | 050 Lamp5 Lhx6 Gaba | 26 |
| 24 | 300 PARN-MDRNd-NTS Gbx2 Gly-Gaba | 25 |
| 44 | 317 Astro-CB NN | 24 |
| 110 | 036 HPF CR Glut | 23 |
| 148 | 001 CLA-EPd-CTX Car3 Glut | 22 |
| 65 | 027 L6b EPd Glut | 22 |
| 137 | 047 Sncg Gaba | 22 |
| 13 | 305 SPVI-SPVC Sall3 Nfib Gly-Gaba | 21 |
| 216 | 085 SI-MPO-LPO Lhx8 Gaba | 21 |
| 213 | 074 MEA-BST Lhx6 Sp9 Gaba | 20 |
| 67 | 029 L6b CTX Glut | 19 |
| 241 | 113 MEA-COA-BMA Ccdc42 Glut | 19 |
| 109 | 053 Sst Gaba | 19 |
| 9 | 255 SPVO Mafa Meis2 Glut | 19 |
| 28 | 243 PGRN-PARN-MDRN Hoxb5 Glut | 19 |
| 49 | 322 Tanycyte NN | 19 |
| 19 | 279 PSV Pax2 Gly-Gaba | 18 |
| 135 | 041 OB-in Frmd7 Gaba | 17 |
| 159 | 336 Monocytes NN | 17 |
| 132 | 005 L5 IT CTX Glut | 16 |
| 133 | 054 STR Prox1 Lhx6 Gaba | 16 |
| 102 | 045 OB-STR-CTX Inh IMN | 16 |
| 12 | 101 ZI Pax6 Gaba | 15 |
| 11 | 278 NLL Gata3 Gly-Gaba | 15 |
| 15 | 254 VCO Mafa Meis2 Glut | 15 |
| 48 | 216 MB-MY Tph2 Glut-Sero | 14 |
| 146 | 032 L5 NP CTX Glut | 14 |
| 115 | 014 LA-BLA-BMA-PA Glut | 14 |
| 125 | 039 OB Meis2 Thsd7b Gaba | 14 |
| 158 | 199 PAG-MRN-RN Foxa2 Gaba | 13 |
| 149 | 200 PAG-ND-PCG Onecut1 Gaba | 13 |
| 45 | 222 PB Evx2 Glut | 13 |
| 66 | 031 CT SUB Glut | 13 |
| 30 | 210 PRT Mecom Gaba | 13 |
| 220 | 098 AHN-SBPV-PVHd Pdrm12 Gaba | 13 |
| 33 | 201 PAG-RN Nkx2-2 Otx1 Gaba | 11 |
| 95 | 323 Ependymal NN | 11 |
| 166 | 066 NDB-SI-ant Prdm12 Gaba | 11 |
| 114 | 015 ENTmv-PA-COAp Glut | 11 |
| 105 | 315 DCO UBC Glut | 11 |
| 38 | 228 PSV Pvalb Lhx2 Glut | 10 |
| 103 | 072 LSX Sall3 Lmo1 Gaba | 10 |
| 31 | 022 L5 ET CTX Glut | 10 |
| 214 | 065 IA Mgp Gaba | 9 |
| 25 | 246 CU-ECU-SPVI Foxb1 Glut | 9 |
| 23 | 264 PRNc Otp Gly-Gaba | 9 |
| 218 | 059 GPe-SI Sox6 Cyp26b1 Gaba | 9 |
| 161 | 055 STR Lhx8 Gaba | 9 |
| 223 | 088 BST Tac2 Gaba | 9 |
| 195 | 051 Pvalb chandelier Gaba | 9 |
| 17 | 235 PG-TRN-LRN Fat2 Glut | 9 |
| 145 | 034 NP PPP Glut | 8 |
| 10 | 020 L2/3 IT RSP Glut | 8 |
| 47 | 217 PB Lmx1a Glut | 8 |
| 210 | 203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba | 8 |
| 167 | 198 IC Six3 En2 Gaba | 8 |
| 189 | 188 SCop Sln Glut | 8 |
| 16 | 181 IC Tfap2d Maf Glut | 8 |
| 239 | 075 MEA-BST Lhx6 Nr2e1 Gaba | 8 |
| 190 | 090 BST-MPN Six3 Nrgn Gaba | 8 |
| 36 | 277 DTN-LDT-IPN Otp Pax3 Gaba | 7 |
| 35 | 224 PCG-PRNr Vsx2 Nkx6-1 Glut | 7 |
| 201 | 151 TH Prkcd Grin2c Glut | 7 |
| 185 | 003 L5/6 IT TPE-ENT Glut | 7 |
| 168 | 079 CEA-BST Six3 Cyp26b1 Gaba | 7 |
| 153 | 082 CEA-BST Ebf1 Pdyn Gaba | 6 |
| 129 | 089 PVR Six3 Sox3 Gaba | 6 |
| 26 | 282 POR Spp1 Gly-Gaba | 6 |
| 208 | 038 DG-PIR Ex IMN | 6 |
| 182 | 081 ACB-BST-FS D1 Gaba | 6 |
| 200 | 195 SNr-VTA Pax5 Npas1 Gaba | 6 |
| 151 | 071 LSX Prdm12 Zeb2 Gaba | 6 |
| 221 | 202 PRT Tcf7l2 Gaba | 6 |
| 217 | 078 SI-MA-ACB Ebf1 Bnc2 Gaba | 6 |
| 97 | 263 CS-RPO Meis2 Gaba | 6 |
| 123 | 265 PB Sst Gly-Gaba | 6 |
| 75 | 002 IT EP-CLA Glut | 6 |
| 93 | 093 RT-ZI Gnb3 Gaba | 6 |
| 118 | 011 L2 IT ENT-po Glut | 6 |
| 58 | 316 Bergmann NN | 6 |
| 107 | 271 NI-RPO Gata3 Nr4a2 Gaba | 5 |
| 89 | 308 DCO Il22 Gly-Gaba | 5 |
| 226 | 084 BST-SI-AAA Six3 Slc22a3 Gaba | 5 |
| 87 | 134 PH-ant-LHA Otp Bsx Glut | 5 |
| 113 | 314 CB Granule Glut | 5 |
| 41 | 238 NTS Phox2b Glut | 5 |
| 121 | 283 PRP Otp Gly-Gaba | 5 |
| 160 | 068 LSX Otx2 Gaba | 5 |
| 22 | 297 CU-ECU Pax2 Gly-Gaba | 5 |
| 78 | 209 SCs Pax7 Nfia Gaba | 4 |
| 83 | 115 MS-SF Bsx Glut | 4 |
| 152 | 008 L2/3 IT ENT Glut | 4 |
| 56 | 261 HB Calcb Chol | 4 |
| 99 | 182 CUN-PPN Evx2 Meis2 Glut | 4 |
| 184 | 324 Hypendymal NN | 4 |
| 77 | 121 MEA-BST Otp Zic2 Glut | 4 |
| 117 | 018 L2 IT PPP-APr Glut | 4 |
| 186 | 024 L5 PPP Glut | 4 |
| 142 | 251 NTS Dbh Glut | 4 |
| 177 | 108 ARH-PVp Tbx3 Gaba | 4 |
| 179 | 270 LDT-DTN Gata3 Nfix Gaba | 4 |
| 227 | 086 MPO-ADP Lhx8 Gaba | 3 |
| 43 | 141 PH-SUM Foxa1 Glut | 3 |
| 209 | 083 CEA-BST Rai14 Pdyn Crh Gaba | 3 |
| 176 | 207 SCs Dmbx1 Gaba | 3 |
| 207 | 102 DMH-LHA Gsx1 Gaba | 3 |
| 191 | 123 DMH Nkx2-4 Glut | 3 |
| 173 | 040 OB Trdn Gaba | 3 |
| 98 | 205 SC-PAG Lef1 Emx2 Gaba | 3 |
| 141 | 234 MEV Ppp1r1c Glut | 3 |
| 131 | 287 MV-SPIV-PRP Dmbx1 Gly-Gaba | 3 |
| 199 | 196 PAG-PPN Pax5 Sox21 Gaba | 3 |
| 59 | 142 HY Gnrh1 Glut | 3 |
| 52 | 162 CUN Evx2 Lhx2 Glut | 3 |
| 197 | 325 CHOR NN | 3 |
| 139 | 168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut | 3 |
| 156 | 214 IPN Otp Crisp1 Gaba | 3 |
| 21 | 221 LDT-PCG Vsx2 Lhx4 Glut | 3 |
| 240 | 215 SNc-VTA-RAmb Foxa1 Dopa | 3 |
| 40 | 229 PB-NTS Phox2b Ebf3 Lmx1b Glut | 3 |
| 183 | 232 LDT Vsx2 Nkx6-1 Nfib Glut | 3 |
| 157 | 147 AD Serpinb7 Glut | 3 |
| 246 | 106 PVpo-VMPO-MPN Hmx2 Gaba | 2 |
| 50 | 267 CS-PRNr-PCG Tmem163 Otp Gaba | 2 |
| 203 | 104 TU-ARH Otp Six6 Gaba | 2 |
| 193 | 172 PAG Pou4f1 Ebf2 Glut | 2 |
| 76 | 293 PAS-MV Ebf2 Gly-Gaba | 2 |
| 196 | 124 MPN-MPO-PVpo Hmx2 Glut | 2 |
| 165 | 313 CBX Purkinje Gaba | 2 |
| 206 | 136 PMv-TMv Pitx2 Glut | 2 |
| 55 | 109 LGv-ZI Otx2 Gaba | 2 |
| 124 | 208 SC Lef1 Otx2 Gaba | 2 |
| 136 | 194 MRN-VTN-PPN Pax5 Cdh23 Gaba | 2 |
| 237 | 116 AVPV-MEPO-SFO Tbr1 Glut | 2 |
| 60 | 256 SPVC Mafa Glut | 2 |
| 37 | 176 SCig Foxb1 Glut | 2 |
| 147 | 192 PPN-CUN-PCG Otp En1 Gaba | 2 |
| 162 | 094 SCH Six6 Cdc14a Gaba | 2 |
| 180 | 275 PDTg Otp Olig3 Gaba | 2 |
| 212 | 092 TMv-PMv Tbx3 Hist-Gaba | 2 |
| 169 | 206 SCm-PAG Cdh23 Gaba | 2 |
| 242 | 103 PVHd-DMH Lhx6 Gaba | 2 |
| 130 | 299 MARN-PPY Ngfr Gly-Gaba | 2 |
| 219 | 193 MRN-PPN-CUN Pax8 Gaba | 1 |
| 247 | 169 PAG-SC Pou4f1 Zic1 Glut | 1 |
| 222 | 268 CS-PRNr-DR En1 Sox2 Gaba | 1 |
| 235 | 273 PDTg-PCG Pax6 Gaba | 1 |
| 248 | 097 PVHd-SBPV Six3 Prox1 Gaba | 1 |
| 224 | 274 PDTg Otp Shroom3 Gaba | 1 |
| 225 | 100 AHN Onecut3 Gaba | 1 |
| 245 | 140 PMd-LHA Foxb1 Glut | 1 |
| 244 | 122 LHA-MEA Otp Glut | 1 |
| 228 | 118 ADP-MPO Trp73 Glut | 1 |
| 229 | 157 RN Spp1 Glut | 1 |
| 230 | 067 LSX Sall3 Pax6 Gaba | 1 |
| 243 | 191 PAG-MRN Rln3 Gaba | 1 |
| 231 | 174 PAG Pou4f2 Mesi2 Glut | 1 |
| 232 | 288 MDRN Hoxb5 Ebf2 Gly-Gaba | 1 |
| 251 | 137 PH-an Pitx2 Glut | 1 |
| 250 | 107 DMH Hmx2 Gaba | 1 |
| 234 | 155 PRC-PAG Pax6 Glut | 1 |
| 236 | 161 PAG Pou4f3 Glut | 1 |
| 233 | 096 PVHd Gsc Gaba | 1 |
| 126 | 257 SPVC Ccdc172 Glut | 1 |
| 211 | 111 TRS-BAC Sln Glut | 1 |
| 86 | 171 PAG Pou4f1 Bnc2 Glut | 1 |
| 119 | 302 MV Xdh Gly-Gaba | 1 |
| 111 | 185 SCig Tfap2b Chrnb3 Glut | 1 |
| 104 | 262 Pineal Crx Glut | 1 |
| 96 | 260 MDRNv Crp Glut | 1 |
| 91 | 220 PB Pax5 Glut | 1 |
| 88 | 248 MV-SPIV Zic4 Neurod2 Glut | 1 |
| 84 | 133 PVH-SO-PVa Otp Glut | 1 |
| 205 | 197 SNr Six3 Gaba | 1 |
| 81 | 177 SCig-an-PPT Foxb1 Glut | 1 |
| 54 | 303 IRN Dmbx1 Pax2 Gly-Gaba | 1 |
| 53 | 187 SCsg Pde5a Glut | 1 |
| 51 | 042 OB-out Frmd7 Gaba | 1 |
| 39 | 160 PAG-SC Neurod2 Meis2 Glut | 1 |
| 18 | 245 SPVI-SPVC Tlx3 Ebf3 Glut | 1 |
| 120 | 301 MV Nr4a2 Gly-Gaba | 1 |
| 122 | 218 PSV Lmx1a Trpv6 Glut | 1 |
| 128 | 226 PRNc-PARN Tlx1 Glut | 1 |
| 138 | 146 LH Pou4f1 Sox1 Glut | 1 |
| 143 | 212 SCs Lef1 Gli3 Gaba | 1 |
| 163 | 276 LDT-PCG St18 Gaba | 1 |
| 164 | 099 SBPV-PVa Six6 Satb2 Gaba | 1 |
| 175 | 309 CB PLI Gly-Gaba | 1 |
| 178 | 044 OB Dopa-Gaba | 1 |
| 181 | 310 CBX Golgi Gly-Gaba | 1 |
| 187 | 021 L4 RSP-ACA Glut | 1 |
| 188 | 312 CBX MLI Cdh22 Gaba | 1 |
| 192 | 091 ARH-PVi Six6 Dopa-Gaba | 1 |
| 194 | 307 RO-RPA Pkd2l1 Gaba | 1 |
| 198 | 213 SCsg Gabrr2 Gaba | 1 |
| 202 | 269 LDT Fgf7 Gaba | 1 |
| 204 | 272 LDT-PCG-CS Gata3 Lhx1 Gaba | 1 |
| 252 | 117 LHA Barhl2 Glut | 1 |
4.3 Microglia (GFP-cre v.s. GFP)
Here, we use Wilcoxon rank-sum to compute differential expression in Microglia cells.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.
Cell number: ‘GFP’: 823, ‘GFP-cre’: 281.
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 499 | Apoe | -17.528004 | -72.127530 | 0.0000000 | 0.0000000 |
| 480 | Lgals3 | -4.536480 | -28.341877 | 0.0000057 | 0.0000540 |
| 497 | Cd74 | -16.465313 | -19.163769 | 0.0000000 | 0.0000000 |
| 1 | Selplg | 16.442451 | 17.481213 | 0.0000000 | 0.0000000 |
| 2 | Cx3cr1 | 15.344980 | 14.605617 | 0.0000000 | 0.0000000 |
| 6 | Csf1r | 11.373759 | 14.508338 | 0.0000000 | 0.0000000 |
| 0 | Tmem119 | 16.584064 | 12.313411 | 0.0000000 | 0.0000000 |
| 498 | C4b | -16.541048 | -8.793243 | 0.0000000 | 0.0000000 |
| 3 | Camk2a | 14.138077 | 7.035869 | 0.0000000 | 0.0000000 |
| 489 | Spp1 | -7.356597 | -6.286214 | 0.0000000 | 0.0000000 |
| 493 | Cst7 | -9.361928 | -6.133037 | 0.0000000 | 0.0000000 |
| 496 | C3 | -11.357290 | -6.061773 | 0.0000000 | 0.0000000 |
| 483 | Ctss | -5.248227 | -5.967553 | 0.0000002 | 0.0000017 |
| 469 | Serpina3n | -3.086549 | -5.700789 | 0.0020249 | 0.0116376 |
| 484 | Itgal | -5.526251 | -5.425139 | 0.0000000 | 0.0000004 |
| 487 | Cxcl2 | -6.669879 | -4.750733 | 0.0000000 | 0.0000000 |
| 8 | Hpca | 8.956267 | 4.728704 | 0.0000000 | 0.0000000 |
| 495 | Csf1 | -9.549914 | -4.433841 | 0.0000000 | 0.0000000 |
| 492 | Gpc3 | -8.764381 | -4.430273 | 0.0000000 | 0.0000000 |
| 5 | P2ry12 | 11.937934 | 4.316917 | 0.0000000 | 0.0000000 |
| 4 | Siglech | 13.443882 | 4.149309 | 0.0000000 | 0.0000000 |
| 490 | Itgax | -7.457363 | -3.879903 | 0.0000000 | 0.0000000 |
| 478 | Clec7a | -4.175785 | -3.712173 | 0.0000297 | 0.0002605 |
| 486 | Xdh | -6.638675 | -3.633732 | 0.0000000 | 0.0000000 |
| 13 | Syp | 7.837777 | 3.564786 | 0.0000000 | 0.0000000 |
| 481 | Ctsb | -4.550565 | -3.408067 | 0.0000054 | 0.0000525 |
| 20 | Rph3a | 6.482435 | 3.402979 | 0.0000000 | 0.0000000 |
| 491 | Rgs12 | -8.487657 | -3.384927 | 0.0000000 | 0.0000000 |
| 14 | Slc17a7 | 7.487700 | 3.303649 | 0.0000000 | 0.0000000 |
| 9 | Cplx1 | 8.825599 | 3.252274 | 0.0000000 | 0.0000000 |
| 16 | Syn1 | 7.200791 | 3.247201 | 0.0000000 | 0.0000000 |
| 482 | Col6a1 | -5.245410 | -3.226926 | 0.0000002 | 0.0000017 |
| 17 | Dnm1 | 7.082040 | 3.181284 | 0.0000000 | 0.0000000 |
| 55 | Mrc2 | 3.091966 | 3.176309 | 0.0019884 | 0.0115602 |
| 52 | Gm2115 | 3.202807 | 3.138704 | 0.0013609 | 0.0082985 |
| 494 | Ly9 | -9.499098 | -3.092839 | 0.0000000 | 0.0000000 |
| 472 | Egr2 | -3.395019 | -3.054615 | 0.0006862 | 0.0045147 |
| 488 | Ddit3 | -6.903155 | -3.015658 | 0.0000000 | 0.0000000 |
| 476 | Fmo1 | -3.845645 | -2.879638 | 0.0001202 | 0.0009393 |
| 18 | Eno2 | 7.021473 | 2.878296 | 0.0000000 | 0.0000000 |
| 7 | Dlg4 | 10.673281 | 2.744821 | 0.0000000 | 0.0000000 |
| 19 | Nptxr | 6.663053 | 2.616900 | 0.0000000 | 0.0000000 |
| 24 | Nefm | 5.845124 | 2.589533 | 0.0000000 | 0.0000001 |
| 15 | Cd14 | 7.393870 | 2.519958 | 0.0000000 | 0.0000000 |
| 11 | Trem2 | 8.236611 | 2.515758 | 0.0000000 | 0.0000000 |
| 25 | Fam131a | 5.676424 | 2.458847 | 0.0000000 | 0.0000002 |
| 477 | Kit | -4.057251 | -2.457241 | 0.0000497 | 0.0004004 |
| 10 | Bin1 | 8.631220 | 2.420129 | 0.0000000 | 0.0000000 |
| 49 | Grin2b | 3.255682 | 2.413346 | 0.0011312 | 0.0071595 |
| 475 | Pdgfrb | -3.687454 | -2.394347 | 0.0002265 | 0.0016414 |
| 485 | Gfap | -6.031810 | -2.383025 | 0.0000000 | 0.0000000 |
| 66 | Cck | 2.626606 | 2.343021 | 0.0086241 | 0.0431206 |
| 31 | Gria2 | 4.640929 | 2.339874 | 0.0000035 | 0.0000347 |
| 468 | Neu4 | -3.034107 | -2.295382 | 0.0024125 | 0.0135533 |
| 26 | Grin1 | 5.509891 | 2.208000 | 0.0000000 | 0.0000004 |
| 59 | Grin2a | 2.914598 | 2.178512 | 0.0035615 | 0.0193558 |
| 12 | Abi3 | 7.988383 | 2.163797 | 0.0000000 | 0.0000000 |
| 30 | Gria1 | 4.849610 | 2.152534 | 0.0000012 | 0.0000126 |
| 58 | Prkce | 2.928359 | 2.142892 | 0.0034076 | 0.0187229 |
| 60 | Nptx1 | 2.845038 | 2.141026 | 0.0044406 | 0.0238743 |
| 45 | Cspg5 | 3.444427 | 2.079186 | 0.0005723 | 0.0039741 |
| 67 | Vgf | 2.620863 | 2.049634 | 0.0087707 | 0.0434196 |
| 34 | Ecscr | 4.245887 | 2.037883 | 0.0000218 | 0.0001944 |
| 43 | Bsg | 3.738053 | 2.031445 | 0.0001855 | 0.0013636 |
| 50 | Adrb1 | 3.235854 | 2.008732 | 0.0012128 | 0.0075491 |
| 42 | S100b | 3.759615 | 2.003029 | 0.0001702 | 0.0012700 |
| 470 | Atf3 | -3.195331 | -1.986412 | 0.0013967 | 0.0084139 |
| 39 | Pecam1 | 3.956594 | 1.968960 | 0.0000760 | 0.0006034 |
| 47 | Dkk3 | 3.398812 | 1.828204 | 0.0006768 | 0.0045120 |
| 479 | Itpr2 | -4.286410 | -1.825444 | 0.0000182 | 0.0001651 |
| 22 | Syngap1 | 6.062256 | 1.809762 | 0.0000000 | 0.0000000 |
| 32 | Bcan | 4.544823 | 1.807302 | 0.0000055 | 0.0000529 |
| 27 | Tgfbr1 | 5.445206 | 1.792527 | 0.0000001 | 0.0000006 |
| 473 | Cd83 | -3.413114 | -1.791534 | 0.0006423 | 0.0043395 |
| 54 | Nnat | 3.119595 | 1.783232 | 0.0018110 | 0.0106529 |
| 33 | Rbfox3 | 4.478622 | 1.743174 | 0.0000075 | 0.0000696 |
| 53 | Lynx1 | 3.183738 | 1.693879 | 0.0014539 | 0.0086540 |
| 471 | Sulf2 | -3.321992 | -1.678094 | 0.0008938 | 0.0058037 |
| 57 | App | 2.976141 | 1.634580 | 0.0029190 | 0.0162167 |
| 64 | Cpne6 | 2.719894 | 1.541622 | 0.0065303 | 0.0333177 |
| 36 | Arc | 4.104058 | 1.465963 | 0.0000406 | 0.0003440 |
| 29 | Spi1 | 4.964568 | 1.396813 | 0.0000007 | 0.0000072 |
| 474 | Bcl11b | -3.664701 | -1.330140 | 0.0002476 | 0.0017688 |
| 28 | Mapt | 5.120700 | 1.304393 | 0.0000003 | 0.0000032 |
| 21 | Smad3 | 6.094761 | 1.279114 | 0.0000000 | 0.0000000 |
| 46 | Cars | 3.417990 | 1.256600 | 0.0006309 | 0.0043209 |
| 37 | Slc29a1 | 4.081629 | 1.231171 | 0.0000447 | 0.0003712 |
| 23 | Mink1 | 6.002989 | 1.213721 | 0.0000000 | 0.0000000 |
| 63 | Adam10 | 2.744815 | 1.082109 | 0.0060545 | 0.0312088 |
| 467 | Bcl6 | -2.766701 | -1.057593 | 0.0056627 | 0.0294930 |
| 40 | Fam107a | 3.778468 | 1.031091 | 0.0001578 | 0.0012138 |
4.4 Endothelia cells (GFP-cre v.s. GFP)
Here, we use Wilcoxon rank-sum to compute differential expression in Endothelia cells.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.
Cell number: ‘GFP-cre’: 604, ‘GFP’: 359}.
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 5 | Bsg | 10.653444 | 21.027288 | 0.0000000 | 0.0000000 |
| 9 | Cldn5 | 8.154539 | 6.750578 | 0.0000000 | 0.0000000 |
| 499 | Cd74 | -8.856686 | -5.983113 | 0.0000000 | 0.0000000 |
| 0 | Flt1 | 13.857852 | 5.898455 | 0.0000000 | 0.0000000 |
| 493 | Serpina3n | -3.326124 | -4.380862 | 0.0008806 | 0.0078627 |
| 2 | Mfsd2a | 12.394976 | 3.826172 | 0.0000000 | 0.0000000 |
| 11 | Camk2a | 8.049234 | 3.741868 | 0.0000000 | 0.0000000 |
| 4 | Car4 | 10.844166 | 3.504257 | 0.0000000 | 0.0000000 |
| 1 | Ctnnb1 | 12.959113 | 3.285085 | 0.0000000 | 0.0000000 |
| 31 | Nefm | 4.899336 | 3.278133 | 0.0000010 | 0.0000141 |
| 498 | Ctss | -6.017189 | -3.232218 | 0.0000000 | 0.0000000 |
| 43 | Agt | 3.595075 | 3.195496 | 0.0003243 | 0.0032430 |
| 3 | Klf2 | 10.876991 | 3.124009 | 0.0000000 | 0.0000000 |
| 24 | App | 5.366796 | 3.086241 | 0.0000001 | 0.0000015 |
| 17 | Cplx1 | 6.886697 | 3.000003 | 0.0000000 | 0.0000000 |
| 496 | C4b | -4.576116 | -2.965848 | 0.0000047 | 0.0000623 |
| 10 | Rgs5 | 8.106259 | 2.892172 | 0.0000000 | 0.0000000 |
| 39 | Slc17a7 | 3.925124 | 2.840441 | 0.0000867 | 0.0009851 |
| 497 | Ppp1r1b | -4.646199 | -2.761572 | 0.0000034 | 0.0000470 |
| 21 | Rph3a | 6.049176 | 2.703232 | 0.0000000 | 0.0000000 |
| 6 | Nos3 | 9.956928 | 2.617786 | 0.0000000 | 0.0000000 |
| 42 | Olig1 | 3.602023 | 2.608540 | 0.0003158 | 0.0032219 |
| 45 | Nnat | 3.465212 | 2.580837 | 0.0005298 | 0.0050944 |
| 28 | S100b | 5.230343 | 2.511027 | 0.0000002 | 0.0000027 |
| 30 | Gria1 | 4.916108 | 2.484843 | 0.0000009 | 0.0000134 |
| 8 | Stard8 | 8.474764 | 2.339496 | 0.0000000 | 0.0000000 |
| 33 | Ndnf | 4.629307 | 2.231720 | 0.0000037 | 0.0000496 |
| 20 | Bcan | 6.056244 | 2.217539 | 0.0000000 | 0.0000000 |
| 495 | C1qa | -3.902841 | -2.194318 | 0.0000951 | 0.0010563 |
| 23 | Syp | 5.461078 | 2.172042 | 0.0000000 | 0.0000009 |
| 491 | Gfap | -3.198178 | -2.098706 | 0.0013830 | 0.0115249 |
| 47 | Syn1 | 3.397285 | 2.076509 | 0.0006806 | 0.0061979 |
| 492 | Penk | -3.275449 | -2.040568 | 0.0010549 | 0.0090943 |
| 40 | Hpca | 3.820059 | 2.027786 | 0.0001334 | 0.0014502 |
| 56 | Ntrk2 | 2.847044 | 1.943510 | 0.0044127 | 0.0334297 |
| 7 | Lef1 | 8.986549 | 1.924718 | 0.0000000 | 0.0000000 |
| 22 | Pecam1 | 5.743446 | 1.908737 | 0.0000000 | 0.0000002 |
| 12 | Klf4 | 7.963458 | 1.892956 | 0.0000000 | 0.0000000 |
| 35 | Dnm1 | 4.233369 | 1.819683 | 0.0000230 | 0.0002878 |
| 41 | Cspg5 | 3.796339 | 1.812952 | 0.0001468 | 0.0015622 |
| 14 | Rapgef3 | 7.681569 | 1.723038 | 0.0000000 | 0.0000000 |
| 18 | Gja1 | 6.333461 | 1.709328 | 0.0000000 | 0.0000000 |
| 13 | Tek | 7.846414 | 1.670759 | 0.0000000 | 0.0000000 |
| 38 | Bin1 | 4.066847 | 1.630963 | 0.0000477 | 0.0005541 |
| 34 | Eno2 | 4.473687 | 1.604909 | 0.0000077 | 0.0000986 |
| 53 | Adam17 | 2.964209 | 1.595523 | 0.0030346 | 0.0240843 |
| 50 | Mapt | 3.210757 | 1.571966 | 0.0013239 | 0.0112191 |
| 19 | Zbtb20 | 6.285900 | 1.508614 | 0.0000000 | 0.0000000 |
| 16 | Rgs12 | 6.926111 | 1.493056 | 0.0000000 | 0.0000000 |
| 54 | Synpo2 | 2.951750 | 1.460817 | 0.0031598 | 0.0246859 |
| 15 | Degs2 | 6.965525 | 1.385835 | 0.0000000 | 0.0000000 |
| 29 | Dlg4 | 5.222436 | 1.373153 | 0.0000002 | 0.0000028 |
| 60 | Fam131a | 2.701368 | 1.336147 | 0.0069055 | 0.0493250 |
| 494 | Bgn | -3.604300 | -1.297905 | 0.0003130 | 0.0032219 |
| 25 | Sema3c | 5.358649 | 1.265677 | 0.0000001 | 0.0000015 |
| 58 | Trpm4 | 2.747611 | 1.236203 | 0.0060031 | 0.0435805 |
| 27 | Mink1 | 5.310250 | 1.208434 | 0.0000001 | 0.0000018 |
| 36 | Fermt2 | 4.151425 | 1.206600 | 0.0000330 | 0.0004006 |
| 48 | Map4k3 | 3.396806 | 1.186127 | 0.0006818 | 0.0061979 |
| 37 | Tshz1 | 4.147233 | 1.123684 | 0.0000337 | 0.0004006 |
| 49 | Fn1 | 3.320493 | 1.099788 | 0.0008986 | 0.0078823 |
| 26 | Cdh5 | 5.336246 | 1.084284 | 0.0000001 | 0.0000016 |
| 51 | Lynx1 | 3.090478 | 1.031523 | 0.0019983 | 0.0163799 |
| 32 | Adgrl2 | 4.731137 | 1.028183 | 0.0000022 | 0.0000319 |
4.5 CA1 Glut (GFP-cre v.s. GFP)
Here, we use Wilcoxon rank-sum to compute differential expression in CA1 Glut cells.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.
Cell number: ‘GFP-cre’: 674, ‘GFP’: 71.
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 4 | Hpca | 6.087094 | 16.628431 | 0.0000000 | 0.0000001 |
| 19 | Gria1 | 3.828857 | 14.512842 | 0.0001287 | 0.0025497 |
| 0 | Fam131a | 7.402612 | 12.221754 | 0.0000000 | 0.0000000 |
| 9 | Camk2a | 4.836512 | 10.497404 | 0.0000013 | 0.0000508 |
| 5 | Syp | 5.781551 | 10.092332 | 0.0000000 | 0.0000004 |
| 29 | Slc17a7 | 3.487368 | 8.949147 | 0.0004878 | 0.0062539 |
| 1 | Fibcd1 | 6.948065 | 7.037974 | 0.0000000 | 0.0000000 |
| 25 | Grin2a | 3.578683 | 6.993995 | 0.0003453 | 0.0049333 |
| 499 | Ctss | -6.984012 | -6.956723 | 0.0000000 | 0.0000000 |
| 18 | Grin2b | 3.958147 | 6.953647 | 0.0000755 | 0.0016420 |
| 23 | Dkk3 | 3.670288 | 6.925179 | 0.0002423 | 0.0036570 |
| 497 | Cd74 | -6.320455 | -6.898205 | 0.0000000 | 0.0000000 |
| 7 | Cx3cl1 | 4.904636 | 6.805468 | 0.0000009 | 0.0000425 |
| 13 | Egr1 | 4.222237 | 6.428306 | 0.0000242 | 0.0006633 |
| 2 | Kcnab1 | 6.723691 | 6.342738 | 0.0000000 | 0.0000000 |
| 3 | Bcan | 6.148261 | 5.659902 | 0.0000000 | 0.0000001 |
| 22 | Cpne6 | 3.692899 | 5.658398 | 0.0002217 | 0.0036543 |
| 30 | Ptk2b | 3.292852 | 5.071836 | 0.0009918 | 0.0123971 |
| 498 | Gfap | -6.401044 | -4.912414 | 0.0000000 | 0.0000000 |
| 17 | Eno2 | 3.997863 | 4.891961 | 0.0000639 | 0.0014527 |
| 20 | Wfs1 | 3.826538 | 4.763576 | 0.0001300 | 0.0025497 |
| 12 | Egr4 | 4.594454 | 3.710779 | 0.0000043 | 0.0001276 |
| 15 | Rbfox3 | 4.129182 | 3.578949 | 0.0000364 | 0.0009101 |
| 32 | Zbtb20 | 3.116020 | 3.459279 | 0.0018331 | 0.0213151 |
| 490 | Cxcl10 | -3.235744 | -3.423799 | 0.0012133 | 0.0147959 |
| 494 | Col6a1 | -3.787983 | -3.412698 | 0.0001519 | 0.0027343 |
| 10 | Kcnd2 | 4.802015 | 3.324475 | 0.0000016 | 0.0000561 |
| 21 | Syn1 | 3.776677 | 3.136939 | 0.0001589 | 0.0027403 |
| 495 | Sulf2 | -3.821610 | -3.003816 | 0.0001326 | 0.0025497 |
| 6 | Prkce | 5.008996 | 2.850744 | 0.0000005 | 0.0000274 |
| 14 | Itga7 | 4.212960 | 2.780114 | 0.0000252 | 0.0006633 |
| 26 | Mink1 | 3.564768 | 2.776180 | 0.0003642 | 0.0050580 |
| 8 | Cck | 4.845789 | 2.774319 | 0.0000013 | 0.0000508 |
| 11 | Nefm | 4.603731 | 2.518946 | 0.0000041 | 0.0001276 |
| 492 | Dclk3 | -3.687391 | -2.135854 | 0.0002266 | 0.0036543 |
| 491 | C1qa | -3.675506 | -2.089087 | 0.0002374 | 0.0036570 |
| 34 | Neurod6 | 3.004702 | 2.080610 | 0.0026584 | 0.0295379 |
| 16 | Htr1a | 4.051492 | 2.009620 | 0.0000509 | 0.0012117 |
| 35 | Adrb1 | 2.940926 | 1.941880 | 0.0032723 | 0.0355687 |
| 27 | Npy2r | 3.509979 | 1.940219 | 0.0004481 | 0.0059547 |
| 496 | Csf1r | -4.693017 | -1.797835 | 0.0000027 | 0.0000897 |
| 28 | Bcl11b | 3.507370 | 1.779664 | 0.0004526 | 0.0059547 |
| 31 | Kcnh7 | 3.179505 | 1.699659 | 0.0014753 | 0.0175627 |
| 24 | Bcl6 | 3.663620 | 1.670695 | 0.0002487 | 0.0036570 |
| 493 | Adgrl2 | -3.785954 | -1.588879 | 0.0001531 | 0.0027343 |
| 33 | Pcdhgc5 | 3.064129 | 1.395493 | 0.0021830 | 0.0248073 |
4.6 CA3 Glut (GFP-cre v.s. GFP)
Here, we use Wilcoxon rank-sum to compute differential expression in CA3 Glut cells.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.
Cell number: ‘GFP-cre’: 594, ‘GFP’: 153.
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 5 | Slc17a7 | 13.829126 | 32.785248 | 0.0000000 | 0.0000000 |
| 142 | Osr1 | 2.956992 | 27.985668 | 0.0031066 | 0.0106389 |
| 7 | Gria1 | 13.361713 | 22.486418 | 0.0000000 | 0.0000000 |
| 2 | Cpne6 | 14.999445 | 20.781628 | 0.0000000 | 0.0000000 |
| 19 | Dnm1 | 10.683278 | 19.660599 | 0.0000000 | 0.0000000 |
| 11 | Hpca | 12.699142 | 18.664454 | 0.0000000 | 0.0000000 |
| 1 | Camk2a | 15.103851 | 18.596859 | 0.0000000 | 0.0000000 |
| 0 | Syp | 15.162251 | 18.328075 | 0.0000000 | 0.0000000 |
| 18 | Nptx1 | 11.201529 | 16.613106 | 0.0000000 | 0.0000000 |
| 3 | Ptk2b | 14.384350 | 16.052973 | 0.0000000 | 0.0000000 |
| 4 | Gria2 | 14.248222 | 14.505323 | 0.0000000 | 0.0000000 |
| 59 | Nptxr | 6.947125 | 12.231750 | 0.0000000 | 0.0000000 |
| 93 | App | 4.741565 | 11.933023 | 0.0000021 | 0.0000110 |
| 37 | Dkk3 | 8.927485 | 10.880051 | 0.0000000 | 0.0000000 |
| 49 | Zbtb20 | 7.788888 | 9.195160 | 0.0000000 | 0.0000000 |
| 6 | Eno2 | 13.470531 | 9.061977 | 0.0000000 | 0.0000000 |
| 12 | Bin1 | 12.509446 | 8.787798 | 0.0000000 | 0.0000000 |
| 8 | Rph3a | 13.161094 | 8.698674 | 0.0000000 | 0.0000000 |
| 15 | Grin2a | 11.632810 | 8.612867 | 0.0000000 | 0.0000000 |
| 45 | Syngap1 | 8.303568 | 8.133543 | 0.0000000 | 0.0000000 |
| 10 | Fam131a | 12.742837 | 7.894958 | 0.0000000 | 0.0000000 |
| 76 | Grin1 | 5.779537 | 7.491878 | 0.0000000 | 0.0000000 |
| 44 | Sema5b | 8.418057 | 7.032755 | 0.0000000 | 0.0000000 |
| 50 | Neurod6 | 7.766830 | 7.016976 | 0.0000000 | 0.0000000 |
| 26 | Grin2b | 9.860842 | 6.775390 | 0.0000000 | 0.0000000 |
| 47 | Bcan | 7.991399 | 6.737943 | 0.0000000 | 0.0000000 |
| 9 | Cx3cl1 | 13.137355 | 6.619198 | 0.0000000 | 0.0000000 |
| 14 | Cck | 11.646045 | 6.614101 | 0.0000000 | 0.0000000 |
| 41 | Itga7 | 8.680860 | 6.470300 | 0.0000000 | 0.0000000 |
| 38 | Syn1 | 8.926645 | 6.377339 | 0.0000000 | 0.0000000 |
| 36 | Plxna1 | 8.990928 | 5.956524 | 0.0000000 | 0.0000000 |
| 121 | Fezf2 | 3.805688 | 5.862751 | 0.0001414 | 0.0005702 |
| 13 | Mink1 | 11.719150 | 5.822962 | 0.0000000 | 0.0000000 |
| 71 | Car4 | 6.112503 | 5.749875 | 0.0000000 | 0.0000000 |
| 34 | Robo1 | 9.132307 | 5.711690 | 0.0000000 | 0.0000000 |
| 134 | Cckbr | 3.291008 | 5.668843 | 0.0009983 | 0.0036170 |
| 32 | Rbfox3 | 9.310239 | 5.637467 | 0.0000000 | 0.0000000 |
| 91 | Iyd | 4.828535 | 5.586290 | 0.0000014 | 0.0000074 |
| 42 | Mapt | 8.654390 | 5.485796 | 0.0000000 | 0.0000000 |
| 156 | Col11a1 | 2.482646 | 5.171348 | 0.0130410 | 0.0404642 |
| 39 | Cspg5 | 8.821818 | 5.129020 | 0.0000000 | 0.0000000 |
| 24 | Neto1 | 9.887731 | 5.117392 | 0.0000000 | 0.0000000 |
| 64 | Arc | 6.766461 | 5.068835 | 0.0000000 | 0.0000000 |
| 94 | Nectin3 | 4.719087 | 5.046242 | 0.0000024 | 0.0000122 |
| 113 | Scn4b | 4.013661 | 5.002230 | 0.0000598 | 0.0002577 |
| 23 | Pcdh9 | 10.425519 | 4.931618 | 0.0000000 | 0.0000000 |
| 25 | Pkp2 | 9.877857 | 4.892412 | 0.0000000 | 0.0000000 |
| 60 | Brinp1 | 6.897337 | 4.834978 | 0.0000000 | 0.0000000 |
| 17 | Ctnnb1 | 11.233460 | 4.821881 | 0.0000000 | 0.0000000 |
| 30 | Npy2r | 9.496574 | 4.758524 | 0.0000000 | 0.0000000 |
| 499 | Col6a1 | -11.018556 | -4.749074 | 0.0000000 | 0.0000000 |
| 21 | Prkce | 10.568579 | 4.696455 | 0.0000000 | 0.0000000 |
| 157 | Crebbp | 2.480756 | 4.675079 | 0.0131104 | 0.0404642 |
| 55 | Chrna7 | 7.352776 | 4.624490 | 0.0000000 | 0.0000000 |
| 29 | Gpr158 | 9.515271 | 4.610660 | 0.0000000 | 0.0000000 |
| 54 | Camk4 | 7.430083 | 4.577786 | 0.0000000 | 0.0000000 |
| 33 | Gria3 | 9.234612 | 4.560895 | 0.0000000 | 0.0000000 |
| 61 | Sulf2 | 6.860994 | 4.472543 | 0.0000000 | 0.0000000 |
| 46 | Nrg3 | 8.218489 | 4.466240 | 0.0000000 | 0.0000000 |
| 22 | Src | 10.440014 | 4.456206 | 0.0000000 | 0.0000000 |
| 35 | Lynx1 | 9.101847 | 4.454622 | 0.0000000 | 0.0000000 |
| 16 | Kcnc1 | 11.360765 | 4.444184 | 0.0000000 | 0.0000000 |
| 132 | Gpr63 | 3.330292 | 4.426542 | 0.0008675 | 0.0031895 |
| 72 | Nos1 | 6.109142 | 4.360443 | 0.0000000 | 0.0000000 |
| 28 | Kcnd2 | 9.596569 | 4.238446 | 0.0000000 | 0.0000000 |
| 53 | Rims1 | 7.543943 | 4.201822 | 0.0000000 | 0.0000000 |
| 128 | Sox8 | 3.504653 | 4.187573 | 0.0004572 | 0.0017318 |
| 40 | Cplx1 | 8.732958 | 4.162605 | 0.0000000 | 0.0000000 |
| 98 | Trpm4 | 4.628545 | 4.137064 | 0.0000037 | 0.0000182 |
| 154 | Olig1 | 2.512057 | 4.101265 | 0.0120030 | 0.0379841 |
| 140 | Enpp2 | 3.115177 | 4.074431 | 0.0018383 | 0.0063831 |
| 80 | Sstr3 | 5.577446 | 4.055631 | 0.0000000 | 0.0000001 |
| 52 | Plp1 | 7.716623 | 4.055600 | 0.0000000 | 0.0000000 |
| 115 | Epha10 | 3.982990 | 4.033365 | 0.0000681 | 0.0002884 |
| 143 | Rspo2 | 2.893340 | 3.943844 | 0.0038117 | 0.0129649 |
| 97 | Nr4a2 | 4.648292 | 3.922088 | 0.0000033 | 0.0000167 |
| 123 | Cdh9 | 3.754220 | 3.891115 | 0.0001739 | 0.0006846 |
| 139 | Kcnh2 | 3.118328 | 3.880388 | 0.0018188 | 0.0063594 |
| 136 | Cpne5 | 3.212231 | 3.869599 | 0.0013171 | 0.0047039 |
| 20 | Pcdhgc5 | 10.653658 | 3.854878 | 0.0000000 | 0.0000000 |
| 145 | Tnik | 2.807210 | 3.847019 | 0.0049973 | 0.0167694 |
| 111 | Adrb1 | 4.096850 | 3.813079 | 0.0000419 | 0.0001837 |
| 131 | Npy1r | 3.334494 | 3.723292 | 0.0008545 | 0.0031650 |
| 152 | Ptpru | 2.532854 | 3.711539 | 0.0113138 | 0.0362622 |
| 75 | Prkcd | 5.801805 | 3.708364 | 0.0000000 | 0.0000000 |
| 89 | Dlg4 | 4.936303 | 3.690283 | 0.0000008 | 0.0000044 |
| 73 | Gng2 | 5.921967 | 3.685230 | 0.0000000 | 0.0000000 |
| 112 | Plcxd2 | 4.080674 | 3.657899 | 0.0000449 | 0.0001952 |
| 27 | Ntng2 | 9.661061 | 3.657227 | 0.0000000 | 0.0000000 |
| 137 | Bace1 | 3.142277 | 3.639369 | 0.0016764 | 0.0059447 |
| 58 | Lrpprc | 7.116444 | 3.603572 | 0.0000000 | 0.0000000 |
| 51 | Pcdhac2 | 7.733429 | 3.503662 | 0.0000000 | 0.0000000 |
| 82 | Egr1 | 5.417160 | 3.460430 | 0.0000001 | 0.0000004 |
| 84 | Psen2 | 5.365693 | 3.451159 | 0.0000001 | 0.0000005 |
| 108 | Prox1 | 4.163023 | 3.403410 | 0.0000314 | 0.0001415 |
| 43 | Camk2g | 8.542842 | 3.382412 | 0.0000000 | 0.0000000 |
| 86 | Mapk1 | 5.039449 | 3.370589 | 0.0000005 | 0.0000027 |
| 99 | Nr4a1 | 4.620143 | 3.363748 | 0.0000038 | 0.0000188 |
| 65 | Epha7 | 6.750706 | 3.333398 | 0.0000000 | 0.0000000 |
| 70 | Gja1 | 6.173004 | 3.330926 | 0.0000000 | 0.0000000 |
| 92 | Grm1 | 4.752699 | 3.327219 | 0.0000020 | 0.0000106 |
| 81 | Rims2 | 5.499509 | 3.322733 | 0.0000000 | 0.0000002 |
| 31 | Sorl1 | 9.407713 | 3.253944 | 0.0000000 | 0.0000000 |
| 138 | Grm3 | 3.139756 | 3.194886 | 0.0016909 | 0.0059538 |
| 90 | Tbr1 | 4.887356 | 3.131626 | 0.0000010 | 0.0000056 |
| 79 | Mas1 | 5.665257 | 3.087153 | 0.0000000 | 0.0000001 |
| 147 | S100b | 2.664990 | 3.065911 | 0.0076991 | 0.0254936 |
| 109 | Gabra1 | 4.147267 | 3.030323 | 0.0000336 | 0.0001502 |
| 57 | Myo5a | 7.211607 | 3.029945 | 0.0000000 | 0.0000000 |
| 77 | Map4k3 | 5.755588 | 3.011587 | 0.0000000 | 0.0000001 |
| 48 | Grb2 | 7.859683 | 2.998926 | 0.0000000 | 0.0000000 |
| 78 | Bsg | 5.728069 | 2.974316 | 0.0000000 | 0.0000001 |
| 107 | Fermt2 | 4.195374 | 2.879404 | 0.0000272 | 0.0001238 |
| 117 | Rasgrf2 | 3.939715 | 2.845032 | 0.0000816 | 0.0003399 |
| 148 | Gad2 | 2.609111 | 2.843162 | 0.0090778 | 0.0298612 |
| 110 | Ntrk2 | 4.104622 | 2.839644 | 0.0000405 | 0.0001792 |
| 69 | Pdgfa | 6.245059 | 2.833634 | 0.0000000 | 0.0000000 |
| 85 | Kctd4 | 5.224313 | 2.665583 | 0.0000002 | 0.0000010 |
| 87 | Slc29a1 | 4.996594 | 2.631637 | 0.0000006 | 0.0000033 |
| 66 | Gphn | 6.689364 | 2.594312 | 0.0000000 | 0.0000000 |
| 103 | Crhr1 | 4.368895 | 2.574274 | 0.0000125 | 0.0000589 |
| 133 | Ngrn | 3.297311 | 2.550913 | 0.0009762 | 0.0035626 |
| 116 | Cnr1 | 3.956941 | 2.532146 | 0.0000759 | 0.0003190 |
| 56 | Ctsb | 7.285973 | 2.512189 | 0.0000000 | 0.0000000 |
| 141 | Slc29a2 | 3.096061 | 2.481938 | 0.0019611 | 0.0067624 |
| 62 | Tcerg1 | 6.854902 | 2.480017 | 0.0000000 | 0.0000000 |
| 102 | Nnat | 4.511535 | 2.445188 | 0.0000064 | 0.0000306 |
| 119 | Pcdhgc3 | 3.873332 | 2.340500 | 0.0001074 | 0.0004400 |
| 101 | Car12 | 4.526450 | 2.317656 | 0.0000060 | 0.0000288 |
| 83 | Psen1 | 5.398464 | 2.302720 | 0.0000001 | 0.0000004 |
| 88 | Cars | 4.978948 | 2.294152 | 0.0000006 | 0.0000036 |
| 63 | Kcnab1 | 6.844819 | 2.268631 | 0.0000000 | 0.0000000 |
| 149 | Gpr83 | 2.601968 | 2.247424 | 0.0092690 | 0.0302910 |
| 67 | Mtor | 6.602184 | 2.230910 | 0.0000000 | 0.0000000 |
| 114 | Syt17 | 3.997065 | 2.218328 | 0.0000641 | 0.0002741 |
| 74 | Smad3 | 5.812939 | 2.204646 | 0.0000000 | 0.0000000 |
| 100 | Tmem150a | 4.587791 | 2.203672 | 0.0000045 | 0.0000217 |
| 104 | Lct | 4.342636 | 2.200770 | 0.0000141 | 0.0000658 |
| 122 | Kit | 3.767665 | 2.196521 | 0.0001648 | 0.0006539 |
| 496 | Cd74 | -2.507225 | -2.167152 | 0.0121683 | 0.0382652 |
| 106 | Bcl11b | 4.239070 | 2.148576 | 0.0000224 | 0.0001030 |
| 118 | Plekhg1 | 3.930892 | 2.075926 | 0.0000846 | 0.0003497 |
| 158 | Adam10 | 2.428868 | 2.060257 | 0.0151461 | 0.0464603 |
| 155 | Rgs12 | 2.504494 | 2.050973 | 0.0122627 | 0.0383208 |
| 498 | Dclk3 | -4.787781 | -2.020220 | 0.0000017 | 0.0000090 |
| 153 | Ccl6 | 2.529283 | 1.987903 | 0.0114296 | 0.0364000 |
| 129 | Lmna | 3.393734 | 1.812827 | 0.0006895 | 0.0025920 |
| 120 | Fam107a | 3.812831 | 1.780631 | 0.0001374 | 0.0005585 |
| 68 | Dapk1 | 6.307662 | 1.722117 | 0.0000000 | 0.0000000 |
| 151 | Gria4 | 2.540206 | 1.710254 | 0.0110787 | 0.0357377 |
| 127 | Nrg2 | 3.574608 | 1.693545 | 0.0003508 | 0.0013388 |
| 124 | Wfs1 | 3.709685 | 1.626378 | 0.0002075 | 0.0008106 |
| 96 | Nrn1 | 4.681694 | 1.624039 | 0.0000028 | 0.0000144 |
| 146 | Lratd2 | 2.672553 | 1.602593 | 0.0075277 | 0.0250922 |
| 144 | Csf1 | 2.852796 | 1.516918 | 0.0043336 | 0.0146407 |
| 126 | Crtac1 | 3.592254 | 1.436591 | 0.0003278 | 0.0012609 |
| 135 | Adgra1 | 3.285967 | 1.422559 | 0.0010163 | 0.0036559 |
| 95 | Snca | 4.687156 | 1.412891 | 0.0000028 | 0.0000141 |
| 125 | Sharpin | 3.625866 | 1.399960 | 0.0002880 | 0.0011163 |
| 130 | Bdnf | 3.384281 | 1.253605 | 0.0007136 | 0.0026629 |
| 150 | Gad1 | 2.550920 | 1.208437 | 0.0107439 | 0.0348828 |
| 497 | Serpina3n | -3.777959 | -1.118605 | 0.0001581 | 0.0006325 |
Abbreviation
Cell types & Regions
Astro, Astrocyte;
ABC, arachnoid barrier cells;
BAM, border-associated macrophages;
BLA, Basolateral amygdala;
CB, cerebellum;
CGE, caudal ganglionic eminence;
CHOR, choroid plexus;
CNU, cerebral nuclei;
CR, Cajal–Retzius;
CT, corticothalamic;
CTX, cerebral cortex;
CTXsp, cortical subplate;
DC, dendritic cells;
DCO, dorsal cochlear nucleus;
DG, dentate gyrus;
EA, extended amygdala;
Endo, endothelial cells;
ENT, Entorhinal area;
ENTl, Entorhinal area, lateral part;
Epen, ependymal;
EPI, epithalamus;
ET, extratelencephalic;
GC, granule cell;
HB, hindbrain;
HPF, hippocampal formation;
HY, hypothalamus;
HYa, anterior hypothalamic;
IMN, immature neurons;
IT, intratelencephalic;
L6b, layer 6b;
LGE, lateral ganglionic eminence;
LH, lateral habenula;
LSX, lateral septal complex;
MB, midbrain;
MGE, medial ganglionic eminence;
MH, medial habenula;
MM, medial mammillary nucleus;
MY, medulla;
NN, non-neuronal;
NP, near-projecting;
NT, non-telencephalon;
OB, olfactory bulb;
OEC, olfactory ensheathing cells;
OLF, olfactory areas;
Oligo, oligodendrocytes;
OPC, oligodendrocyte precursor cells;
P, pons;
PAL, pallidum;
Peri, pericytes;
PIR, piriform cortex;
SMC, smooth muscle cells;
STR, striatum;
TE, telencephalon;
TH, thalamus;
UBC, unipolar brush cells;
VLMC, vascular leptomeningeal cells.
Neurotransmitter types
Chol, cholinergic;
Dopa, dopaminergic;
GABA, GABAergic;
Glut, glutamatergic;
Glyc, glycinergic;
Hist, histaminergic;
Nora, noradrenergic;
Sero, serotonergic